2011-05-19 15:51:33,401 - INFO - Generating QC metrics for BAM File ['WTCHG_11897.bam']
2011-05-19 15:51:33,401 - INFO - Output will go to WTCHG_11897.qc.txt.tmp
2011-05-19 15:51:33,402 - INFO - Reading GC Map from file /data/Genomes/gcMap/Mouse37.gcMap.gz
2011-05-19 15:54:22,310 - INFO - Finished reading GC Map
2011-05-19 15:54:22,310 - INFO - Reading CDS from exon definition file /data/Genomes/annotation/Mouse37.refGene.txt.gz
2011-05-19 15:54:25,067 - INFO - Read 382138 exons (33804740 nucleotides) for 32 chromosomes
2011-05-19 15:54:25,068 - INFO - Computing coverage cut-off
2011-05-19 15:54:25,069 - INFO - Retrieving BAM file coverage info from samtools pileup
2011-05-19 15:54:30,257 - INFO - Processed 1000000 pile-up sites
2011-05-19 15:54:34,594 - INFO - Processed 2000000 pile-up sites
2011-05-19 15:54:38,922 - INFO - Processed 3000000 pile-up sites
2011-05-19 15:54:43,255 - INFO - Processed 4000000 pile-up sites
2011-05-19 15:54:48,089 - INFO - Processed 5000000 pile-up sites
2011-05-19 15:54:52,863 - INFO - Processed 6000000 pile-up sites
2011-05-19 15:54:57,549 - INFO - Processed 7000000 pile-up sites
2011-05-19 15:55:01,740 - INFO - Processed 8000000 pile-up sites
2011-05-19 15:55:06,366 - INFO - Processed 9000000 pile-up sites
2011-05-19 15:55:10,591 - INFO - Processed 10000000 pile-up sites
2011-05-19 15:55:15,127 - INFO - Processed 11000000 pile-up sites
2011-05-19 15:55:19,340 - INFO - Processed 12000000 pile-up sites
2011-05-19 15:55:23,906 - INFO - Processed 13000000 pile-up sites
2011-05-19 15:55:28,087 - INFO - Processed 14000000 pile-up sites
2011-05-19 15:55:32,521 - INFO - Processed 15000000 pile-up sites
2011-05-19 15:55:36,871 - INFO - Processed 16000000 pile-up sites
2011-05-19 15:55:41,314 - INFO - Processed 17000000 pile-up sites
2011-05-19 15:55:45,736 - INFO - Processed 18000000 pile-up sites
2011-05-19 15:55:50,314 - INFO - Processed 19000000 pile-up sites
2011-05-19 15:55:55,101 - INFO - Processed 20000000 pile-up sites
2011-05-19 15:55:59,739 - INFO - Processed 21000000 pile-up sites
2011-05-19 15:56:05,070 - INFO - Processed 22000000 pile-up sites
2011-05-19 15:56:10,549 - INFO - Processed 23000000 pile-up sites
2011-05-19 15:56:16,581 - INFO - Processed 24000000 pile-up sites
2011-05-19 15:56:23,222 - INFO - Processed 25000000 pile-up sites
2011-05-19 15:56:27,722 - INFO - Processed 26000000 pile-up sites
2011-05-19 15:56:32,585 - INFO - Processed 27000000 pile-up sites
2011-05-19 15:56:36,894 - INFO - Processed 28000000 pile-up sites
2011-05-19 15:56:41,030 - INFO - Processed 29000000 pile-up sites
2011-05-19 15:56:46,819 - INFO - Processed 30000000 pile-up sites
2011-05-19 15:56:52,018 - INFO - Processed 31000000 pile-up sites
2011-05-19 15:56:56,624 - INFO - Processed 32000000 pile-up sites
2011-05-19 15:57:01,272 - INFO - Processed 33000000 pile-up sites
2011-05-19 15:57:05,898 - INFO - Processed 34000000 pile-up sites
2011-05-19 15:57:10,188 - INFO - Processed 35000000 pile-up sites
2011-05-19 15:57:14,395 - INFO - Processed 36000000 pile-up sites
2011-05-19 15:57:18,579 - INFO - Processed 37000000 pile-up sites
2011-05-19 15:57:22,912 - INFO - Processed 38000000 pile-up sites
2011-05-19 15:57:27,318 - INFO - Processed 39000000 pile-up sites
2011-05-19 15:57:31,214 - INFO - Finished processing pile-up on 39823502 sites (200000001 nucleotides)
2011-05-19 15:57:31,215 - INFO - Coverage cut-off value is 24
2011-05-19 15:57:31,215 - INFO - Loading data into QC data manager
2011-05-19 15:57:31,553 - INFO - Reading data from BAM file WTCHG_11897.bam. All reads in file will be read
2011-05-19 15:57:31,605 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:2989999-23009999
2011-05-19 15:57:43,223 - INFO - Processed 100000 reads so far
2011-05-19 15:57:54,490 - INFO - Processed 200000 reads so far
2011-05-19 15:58:05,850 - INFO - Processed 300000 reads so far
2011-05-19 15:58:17,160 - INFO - Processed 400000 reads so far
2011-05-19 15:58:28,860 - INFO - Processed 500000 reads so far
2011-05-19 15:58:40,205 - INFO - Processed 600000 reads so far
2011-05-19 15:58:51,541 - INFO - Processed 700000 reads so far
2011-05-19 15:59:02,913 - INFO - Processed 800000 reads so far
2011-05-19 15:59:14,412 - INFO - Processed 900000 reads so far
2011-05-19 15:59:22,915 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:22990009-43010009
2011-05-19 15:59:23,889 - INFO - Processed 1000000 reads so far
2011-05-19 15:59:33,499 - INFO - Processed 1100000 reads so far
2011-05-19 15:59:45,047 - INFO - Processed 1200000 reads so far
2011-05-19 15:59:56,949 - INFO - Processed 1300000 reads so far
2011-05-19 16:00:06,147 - INFO - Processed 1400000 reads so far
2011-05-19 16:00:16,532 - INFO - Processed 1500000 reads so far
2011-05-19 16:00:26,599 - INFO - Processed 1600000 reads so far
2011-05-19 16:00:37,145 - INFO - Processed 1700000 reads so far
2011-05-19 16:00:48,661 - INFO - Processed 1800000 reads so far
2011-05-19 16:01:03,240 - INFO - Processed 1900000 reads so far
2011-05-19 16:01:08,491 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:42990075-63010075
2011-05-19 16:01:14,241 - INFO - Processed 2000000 reads so far
2011-05-19 16:01:26,254 - INFO - Processed 2100000 reads so far
2011-05-19 16:01:39,743 - INFO - Processed 2200000 reads so far
2011-05-19 16:01:48,935 - INFO - Processed 2300000 reads so far
2011-05-19 16:01:58,806 - INFO - Processed 2400000 reads so far
2011-05-19 16:02:10,102 - INFO - Processed 2500000 reads so far
2011-05-19 16:02:21,705 - INFO - Processed 2600000 reads so far
2011-05-19 16:02:34,270 - INFO - Processed 2700000 reads so far
2011-05-19 16:02:46,400 - INFO - Processed 2800000 reads so far
2011-05-19 16:02:58,726 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:62990076-83010076
2011-05-19 16:02:58,846 - INFO - Processed 2900000 reads so far
2011-05-19 16:03:11,185 - INFO - Processed 3000000 reads so far
2011-05-19 16:03:23,104 - INFO - Processed 3100000 reads so far
2011-05-19 16:03:35,896 - INFO - Processed 3200000 reads so far
2011-05-19 16:03:47,659 - INFO - Processed 3300000 reads so far
2011-05-19 16:04:00,176 - INFO - Processed 3400000 reads so far
2011-05-19 16:04:14,357 - INFO - Processed 3500000 reads so far
2011-05-19 16:04:26,806 - INFO - Processed 3600000 reads so far
2011-05-19 16:04:38,097 - INFO - Processed 3700000 reads so far
2011-05-19 16:04:47,999 - INFO - Processed 3800000 reads so far
2011-05-19 16:04:54,649 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:82990136-103010136
2011-05-19 16:04:57,255 - INFO - Processed 3900000 reads so far
2011-05-19 16:05:07,580 - INFO - Processed 4000000 reads so far
2011-05-19 16:05:20,662 - INFO - Processed 4100000 reads so far
2011-05-19 16:05:31,895 - INFO - Processed 4200000 reads so far
2011-05-19 16:05:43,755 - INFO - Processed 4300000 reads so far
2011-05-19 16:05:57,766 - INFO - Processed 4400000 reads so far
2011-05-19 16:06:09,547 - INFO - Processed 4500000 reads so far
2011-05-19 16:06:21,353 - INFO - Processed 4600000 reads so far
2011-05-19 16:06:33,402 - INFO - Processed 4700000 reads so far
2011-05-19 16:06:45,169 - INFO - Processed 4800000 reads so far
2011-05-19 16:06:49,155 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:102990204-123010204
2011-05-19 16:06:56,273 - INFO - Processed 4900000 reads so far
2011-05-19 16:07:08,675 - INFO - Processed 5000000 reads so far
2011-05-19 16:07:19,870 - INFO - Processed 5100000 reads so far
2011-05-19 16:07:30,125 - INFO - Processed 5200000 reads so far
2011-05-19 16:07:41,757 - INFO - Processed 5300000 reads so far
2011-05-19 16:07:52,871 - INFO - Processed 5400000 reads so far
2011-05-19 16:08:06,346 - INFO - Processed 5500000 reads so far
2011-05-19 16:08:18,637 - INFO - Processed 5600000 reads so far
2011-05-19 16:08:33,591 - INFO - Processed 5700000 reads so far
2011-05-19 16:09:04,302 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr10:122990218-143010218
2011-05-19 16:09:06,330 - INFO - Processed 5800000 reads so far
2011-05-19 16:09:18,299 - INFO - Processed 5900000 reads so far
2011-05-19 16:09:30,286 - INFO - Processed 6000000 reads so far
2011-05-19 16:09:42,226 - INFO - Processed 6100000 reads so far
2011-05-19 16:09:44,267 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:2990005-23010005
2011-05-19 16:09:52,770 - INFO - Processed 6200000 reads so far
2011-05-19 16:10:01,080 - INFO - Processed 6300000 reads so far
2011-05-19 16:10:12,028 - INFO - Processed 6400000 reads so far
2011-05-19 16:10:22,509 - INFO - Processed 6500000 reads so far
2011-05-19 16:10:32,149 - INFO - Processed 6600000 reads so far
2011-05-19 16:10:41,013 - INFO - Processed 6700000 reads so far
2011-05-19 16:10:50,489 - INFO - Processed 6800000 reads so far
2011-05-19 16:10:59,848 - INFO - Processed 6900000 reads so far
2011-05-19 16:11:10,578 - INFO - Processed 7000000 reads so far
2011-05-19 16:11:22,641 - INFO - Processed 7100000 reads so far
2011-05-19 16:11:34,013 - INFO - Processed 7200000 reads so far
2011-05-19 16:11:39,322 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:22990008-43010008
2011-05-19 16:11:45,714 - INFO - Processed 7300000 reads so far
2011-05-19 16:11:54,744 - INFO - Processed 7400000 reads so far
2011-05-19 16:12:06,934 - INFO - Processed 7500000 reads so far
2011-05-19 16:12:17,541 - INFO - Processed 7600000 reads so far
2011-05-19 16:12:27,625 - INFO - Processed 7700000 reads so far
2011-05-19 16:12:36,695 - INFO - Processed 7800000 reads so far
2011-05-19 16:12:49,417 - INFO - Processed 7900000 reads so far
2011-05-19 16:13:05,588 - INFO - Processed 8000000 reads so far
2011-05-19 16:13:17,202 - INFO - Processed 8100000 reads so far
2011-05-19 16:13:28,836 - INFO - Processed 8200000 reads so far
2011-05-19 16:13:28,854 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:42990117-63010117
2011-05-19 16:13:40,634 - INFO - Processed 8300000 reads so far
2011-05-19 16:13:51,327 - INFO - Processed 8400000 reads so far
2011-05-19 16:14:01,562 - INFO - Processed 8500000 reads so far
2011-05-19 16:14:12,002 - INFO - Processed 8600000 reads so far
2011-05-19 16:14:21,552 - INFO - Processed 8700000 reads so far
2011-05-19 16:14:33,293 - INFO - Processed 8800000 reads so far
2011-05-19 16:14:43,457 - INFO - Processed 8900000 reads so far
2011-05-19 16:14:52,995 - INFO - Processed 9000000 reads so far
2011-05-19 16:15:03,618 - INFO - Processed 9100000 reads so far
2011-05-19 16:15:14,744 - INFO - Processed 9200000 reads so far
2011-05-19 16:15:15,209 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:62990188-83010188
2011-05-19 16:15:25,625 - INFO - Processed 9300000 reads so far
2011-05-19 16:15:36,302 - INFO - Processed 9400000 reads so far
2011-05-19 16:15:49,183 - INFO - Processed 9500000 reads so far
2011-05-19 16:16:00,766 - INFO - Processed 9600000 reads so far
2011-05-19 16:16:11,324 - INFO - Processed 9700000 reads so far
2011-05-19 16:16:25,600 - INFO - Processed 9800000 reads so far
2011-05-19 16:16:37,721 - INFO - Processed 9900000 reads so far
2011-05-19 16:17:17,105 - INFO - Processed 10000000 reads so far
2011-05-19 16:17:28,630 - INFO - Processed 10100000 reads so far
2011-05-19 16:17:40,604 - INFO - Processed 10200000 reads so far
2011-05-19 16:17:40,724 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:82990241-103010241
2011-05-19 16:17:53,911 - INFO - Processed 10300000 reads so far
2011-05-19 16:18:05,297 - INFO - Processed 10400000 reads so far
2011-05-19 16:18:16,825 - INFO - Processed 10500000 reads so far
2011-05-19 16:18:28,717 - INFO - Processed 10600000 reads so far
2011-05-19 16:18:41,214 - INFO - Processed 10700000 reads so far
2011-05-19 16:18:55,616 - INFO - Processed 10800000 reads so far
2011-05-19 16:19:06,803 - INFO - Processed 10900000 reads so far
2011-05-19 16:19:19,823 - INFO - Processed 11000000 reads so far
2011-05-19 16:19:32,179 - INFO - Processed 11100000 reads so far
2011-05-19 16:19:41,782 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr11:102990259-123010259
2011-05-19 16:19:46,083 - INFO - Processed 11200000 reads so far
2011-05-19 16:19:57,245 - INFO - Processed 11300000 reads so far
2011-05-19 16:20:09,482 - INFO - Processed 11400000 reads so far
2011-05-19 16:20:20,554 - INFO - Processed 11500000 reads so far
2011-05-19 16:20:33,241 - INFO - Processed 11600000 reads so far
2011-05-19 16:20:44,695 - INFO - Processed 11700000 reads so far
2011-05-19 16:20:56,828 - INFO - Processed 11800000 reads so far
2011-05-19 16:21:09,853 - INFO - Processed 11900000 reads so far
2011-05-19 16:21:21,353 - INFO - Processed 12000000 reads so far
2011-05-19 16:21:34,305 - INFO - Processed 12100000 reads so far
2011-05-19 16:21:37,211 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:2990022-23010022
2011-05-19 16:21:46,220 - INFO - Processed 12200000 reads so far
2011-05-19 16:21:57,538 - INFO - Processed 12300000 reads so far
2011-05-19 16:22:08,678 - INFO - Processed 12400000 reads so far
2011-05-19 16:22:22,547 - INFO - Processed 12500000 reads so far
2011-05-19 16:22:34,627 - INFO - Processed 12600000 reads so far
2011-05-19 16:22:45,735 - INFO - Processed 12700000 reads so far
2011-05-19 16:22:57,218 - INFO - Processed 12800000 reads so far
2011-05-19 16:23:09,097 - INFO - Processed 12900000 reads so far
2011-05-19 16:23:20,241 - INFO - Processed 13000000 reads so far
2011-05-19 16:23:30,942 - INFO - Processed 13100000 reads so far
2011-05-19 16:23:36,389 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:22990213-43010213
2011-05-19 16:23:43,961 - INFO - Processed 13200000 reads so far
2011-05-19 16:23:53,574 - INFO - Processed 13300000 reads so far
2011-05-19 16:24:03,099 - INFO - Processed 13400000 reads so far
2011-05-19 16:24:16,724 - INFO - Processed 13500000 reads so far
2011-05-19 16:24:29,566 - INFO - Processed 13600000 reads so far
2011-05-19 16:24:40,761 - INFO - Processed 13700000 reads so far
2011-05-19 16:24:53,074 - INFO - Processed 13800000 reads so far
2011-05-19 16:25:05,221 - INFO - Processed 13900000 reads so far
2011-05-19 16:25:18,202 - INFO - Processed 14000000 reads so far
2011-05-19 16:25:25,688 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:42990307-63010307
2011-05-19 16:25:31,906 - INFO - Processed 14100000 reads so far
2011-05-19 16:25:44,265 - INFO - Processed 14200000 reads so far
2011-05-19 16:25:56,532 - INFO - Processed 14300000 reads so far
2011-05-19 16:26:08,224 - INFO - Processed 14400000 reads so far
2011-05-19 16:26:20,541 - INFO - Processed 14500000 reads so far
2011-05-19 16:26:32,054 - INFO - Processed 14600000 reads so far
2011-05-19 16:26:44,145 - INFO - Processed 14700000 reads so far
2011-05-19 16:26:56,395 - INFO - Processed 14800000 reads so far
2011-05-19 16:27:07,509 - INFO - Processed 14900000 reads so far
2011-05-19 16:27:18,293 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:62990364-83010364
2011-05-19 16:27:22,429 - INFO - Processed 15000000 reads so far
2011-05-19 16:27:34,402 - INFO - Processed 15100000 reads so far
2011-05-19 16:27:47,676 - INFO - Processed 15200000 reads so far
2011-05-19 16:28:00,129 - INFO - Processed 15300000 reads so far
2011-05-19 16:28:12,857 - INFO - Processed 15400000 reads so far
2011-05-19 16:28:26,321 - INFO - Processed 15500000 reads so far
2011-05-19 16:28:45,436 - INFO - Processed 15600000 reads so far
2011-05-19 16:28:59,206 - INFO - Processed 15700000 reads so far
2011-05-19 16:29:11,035 - INFO - Processed 15800000 reads so far
2011-05-19 16:29:27,135 - INFO - Processed 15900000 reads so far
2011-05-19 16:29:31,620 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:82990404-103010404
2011-05-19 16:29:39,897 - INFO - Processed 16000000 reads so far
2011-05-19 16:29:54,049 - INFO - Processed 16100000 reads so far
2011-05-19 16:30:07,391 - INFO - Processed 16200000 reads so far
2011-05-19 16:30:18,309 - INFO - Processed 16300000 reads so far
2011-05-19 16:30:30,914 - INFO - Processed 16400000 reads so far
2011-05-19 16:30:43,415 - INFO - Processed 16500000 reads so far
2011-05-19 16:30:56,724 - INFO - Processed 16600000 reads so far
2011-05-19 16:31:11,562 - INFO - Processed 16700000 reads so far
2011-05-19 16:31:34,587 - INFO - Processed 16800000 reads so far
2011-05-19 16:31:46,872 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr12:102990430-123010430
2011-05-19 16:31:47,558 - INFO - Processed 16900000 reads so far
2011-05-19 16:32:01,656 - INFO - Processed 17000000 reads so far
2011-05-19 16:32:17,719 - INFO - Processed 17100000 reads so far
2011-05-19 16:32:30,266 - INFO - Processed 17200000 reads so far
2011-05-19 16:32:45,009 - INFO - Processed 17300000 reads so far
2011-05-19 16:32:57,879 - INFO - Processed 17400000 reads so far
2011-05-19 16:33:08,224 - INFO - Processed 17500000 reads so far
2011-05-19 16:33:18,398 - INFO - Processed 17600000 reads so far
2011-05-19 16:33:30,184 - INFO - Processed 17700000 reads so far
2011-05-19 16:33:40,941 - INFO - Processed 17800000 reads so far
2011-05-19 16:33:45,316 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:2990052-23010052
2011-05-19 16:33:53,105 - INFO - Processed 17900000 reads so far
2011-05-19 16:34:12,276 - INFO - Processed 18000000 reads so far
2011-05-19 16:34:25,715 - INFO - Processed 18100000 reads so far
2011-05-19 16:34:36,825 - INFO - Processed 18200000 reads so far
2011-05-19 16:34:51,656 - INFO - Processed 18300000 reads so far
2011-05-19 16:35:04,572 - INFO - Processed 18400000 reads so far
2011-05-19 16:35:14,697 - INFO - Processed 18500000 reads so far
2011-05-19 16:35:26,711 - INFO - Processed 18600000 reads so far
2011-05-19 16:35:36,771 - INFO - Processed 18700000 reads so far
2011-05-19 16:35:46,292 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:22990430-43010430
2011-05-19 16:35:50,073 - INFO - Processed 18800000 reads so far
2011-05-19 16:36:01,767 - INFO - Processed 18900000 reads so far
2011-05-19 16:36:14,008 - INFO - Processed 19000000 reads so far
2011-05-19 16:36:26,172 - INFO - Processed 19100000 reads so far
2011-05-19 16:36:39,367 - INFO - Processed 19200000 reads so far
2011-05-19 16:36:51,462 - INFO - Processed 19300000 reads so far
2011-05-19 16:37:03,027 - INFO - Processed 19400000 reads so far
2011-05-19 16:37:13,953 - INFO - Processed 19500000 reads so far
2011-05-19 16:37:27,235 - INFO - Processed 19600000 reads so far
2011-05-19 16:37:39,459 - INFO - Processed 19700000 reads so far
2011-05-19 16:37:46,720 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:42990431-63010431
2011-05-19 16:37:52,147 - INFO - Processed 19800000 reads so far
2011-05-19 16:38:05,767 - INFO - Processed 19900000 reads so far
2011-05-19 16:38:18,267 - INFO - Processed 20000000 reads so far
2011-05-19 16:38:31,731 - INFO - Processed 20100000 reads so far
2011-05-19 16:40:15,095 - INFO - Processed 20200000 reads so far
2011-05-19 16:40:24,702 - INFO - Processed 20300000 reads so far
2011-05-19 16:40:36,727 - INFO - Processed 20400000 reads so far
2011-05-19 16:40:49,143 - INFO - Processed 20500000 reads so far
2011-05-19 16:41:00,463 - INFO - Processed 20600000 reads so far
2011-05-19 16:41:13,847 - INFO - Processed 20700000 reads so far
2011-05-19 16:41:22,079 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:62990467-83010467
2011-05-19 16:41:27,319 - INFO - Processed 20800000 reads so far
2011-05-19 16:41:38,264 - INFO - Processed 20900000 reads so far
2011-05-19 16:41:50,645 - INFO - Processed 21000000 reads so far
2011-05-19 16:42:03,984 - INFO - Processed 21100000 reads so far
2011-05-19 16:42:15,125 - INFO - Processed 21200000 reads so far
2011-05-19 16:42:26,154 - INFO - Processed 21300000 reads so far
2011-05-19 16:42:37,782 - INFO - Processed 21400000 reads so far
2011-05-19 16:42:47,393 - INFO - Processed 21500000 reads so far
2011-05-19 16:43:00,407 - INFO - Processed 21600000 reads so far
2011-05-19 16:43:12,555 - INFO - Processed 21700000 reads so far
2011-05-19 16:43:13,167 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:82990501-103010501
2011-05-19 16:43:27,870 - INFO - Processed 21800000 reads so far
2011-05-19 16:43:41,046 - INFO - Processed 21900000 reads so far
2011-05-19 16:43:53,169 - INFO - Processed 22000000 reads so far
2011-05-19 16:44:06,127 - INFO - Processed 22100000 reads so far
2011-05-19 16:44:19,559 - INFO - Processed 22200000 reads so far
2011-05-19 16:44:34,066 - INFO - Processed 22300000 reads so far
2011-05-19 16:44:47,448 - INFO - Processed 22400000 reads so far
2011-05-19 16:45:05,371 - INFO - Processed 22500000 reads so far
2011-05-19 16:45:18,110 - INFO - Processed 22600000 reads so far
2011-05-19 16:45:20,308 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13:102990524-123010524
2011-05-19 16:45:32,383 - INFO - Processed 22700000 reads so far
2011-05-19 16:45:45,050 - INFO - Processed 22800000 reads so far
2011-05-19 16:45:56,594 - INFO - Processed 22900000 reads so far
2011-05-19 16:46:06,879 - INFO - Processed 23000000 reads so far
2011-05-19 16:46:25,028 - INFO - Processed 23100000 reads so far
2011-05-19 16:46:42,657 - INFO - Processed 23200000 reads so far
2011-05-19 16:46:54,875 - INFO - Processed 23300000 reads so far
2011-05-19 16:47:06,624 - INFO - Processed 23400000 reads so far
2011-05-19 16:47:13,116 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr13_random:0-20010000
2011-05-19 16:47:14,662 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:2990048-23010048
2011-05-19 16:47:18,510 - INFO - Processed 23500000 reads so far
2011-05-19 16:47:27,838 - INFO - Processed 23600000 reads so far
2011-05-19 16:47:40,270 - INFO - Processed 23700000 reads so far
2011-05-19 16:47:54,252 - INFO - Processed 23800000 reads so far
2011-05-19 16:48:10,559 - INFO - Processed 23900000 reads so far
2011-05-19 16:48:26,494 - INFO - Processed 24000000 reads so far
2011-05-19 16:48:38,282 - INFO - Processed 24100000 reads so far
2011-05-19 16:48:50,523 - INFO - Processed 24200000 reads so far
2011-05-19 16:49:02,023 - INFO - Processed 24300000 reads so far
2011-05-19 16:49:18,145 - INFO - Processed 24400000 reads so far
2011-05-19 16:49:22,851 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:22990061-43010061
2011-05-19 16:49:31,888 - INFO - Processed 24500000 reads so far
2011-05-19 16:49:43,299 - INFO - Processed 24600000 reads so far
2011-05-19 16:49:55,888 - INFO - Processed 24700000 reads so far
2011-05-19 16:50:06,513 - INFO - Processed 24800000 reads so far
2011-05-19 16:50:19,179 - INFO - Processed 24900000 reads so far
2011-05-19 16:50:31,490 - INFO - Processed 25000000 reads so far
2011-05-19 16:50:43,105 - INFO - Processed 25100000 reads so far
2011-05-19 16:50:54,419 - INFO - Processed 25200000 reads so far
2011-05-19 16:51:05,509 - INFO - Processed 25300000 reads so far
2011-05-19 16:51:16,654 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:42990088-63010088
2011-05-19 16:51:17,517 - INFO - Processed 25400000 reads so far
2011-05-19 16:51:27,894 - INFO - Processed 25500000 reads so far
2011-05-19 16:51:38,820 - INFO - Processed 25600000 reads so far
2011-05-19 16:51:50,529 - INFO - Processed 25700000 reads so far
2011-05-19 16:52:03,303 - INFO - Processed 25800000 reads so far
2011-05-19 16:52:13,612 - INFO - Processed 25900000 reads so far
2011-05-19 16:52:24,674 - INFO - Processed 26000000 reads so far
2011-05-19 16:52:40,258 - INFO - Processed 26100000 reads so far
2011-05-19 16:52:55,703 - INFO - Processed 26200000 reads so far
2011-05-19 16:53:08,262 - INFO - Processed 26300000 reads so far
2011-05-19 16:53:20,785 - INFO - Processed 26400000 reads so far
2011-05-19 16:53:21,537 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:62990094-83010094
2011-05-19 16:53:37,819 - INFO - Processed 26500000 reads so far
2011-05-19 16:53:51,300 - INFO - Processed 26600000 reads so far
2011-05-19 16:54:09,684 - INFO - Processed 26700000 reads so far
2011-05-19 16:54:22,641 - INFO - Processed 26800000 reads so far
2011-05-19 16:54:33,985 - INFO - Processed 26900000 reads so far
2011-05-19 16:54:48,531 - INFO - Processed 27000000 reads so far
2011-05-19 16:55:02,063 - INFO - Processed 27100000 reads so far
2011-05-19 16:55:12,209 - INFO - Processed 27200000 reads so far
2011-05-19 16:55:21,492 - INFO - Processed 27300000 reads so far
2011-05-19 16:55:30,576 - INFO - Processed 27400000 reads so far
2011-05-19 16:55:30,751 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:82990107-103010107
2011-05-19 16:55:40,523 - INFO - Processed 27500000 reads so far
2011-05-19 16:55:52,323 - INFO - Processed 27600000 reads so far
2011-05-19 16:56:06,754 - INFO - Processed 27700000 reads so far
2011-05-19 16:56:21,178 - INFO - Processed 27800000 reads so far
2011-05-19 16:56:33,867 - INFO - Processed 27900000 reads so far
2011-05-19 16:56:47,139 - INFO - Processed 28000000 reads so far
2011-05-19 16:56:59,270 - INFO - Processed 28100000 reads so far
2011-05-19 16:57:10,454 - INFO - Processed 28200000 reads so far
2011-05-19 16:57:18,329 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:102990122-123010122
2011-05-19 16:57:22,316 - INFO - Processed 28300000 reads so far
2011-05-19 16:57:34,185 - INFO - Processed 28400000 reads so far
2011-05-19 16:57:47,086 - INFO - Processed 28500000 reads so far
2011-05-19 16:57:58,739 - INFO - Processed 28600000 reads so far
2011-05-19 16:58:11,118 - INFO - Processed 28700000 reads so far
2011-05-19 16:58:21,969 - INFO - Processed 28800000 reads so far
2011-05-19 16:58:31,552 - INFO - Processed 28900000 reads so far
2011-05-19 16:58:41,016 - INFO - Processed 29000000 reads so far
2011-05-19 16:58:54,119 - INFO - Processed 29100000 reads so far
2011-05-19 16:59:05,627 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr14:122990150-143010150
2011-05-19 16:59:05,850 - INFO - Processed 29200000 reads so far
2011-05-19 16:59:17,013 - INFO - Processed 29300000 reads so far
2011-05-19 16:59:17,202 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:2990000-23010000
2011-05-19 16:59:29,931 - INFO - Processed 29400000 reads so far
2011-05-19 16:59:40,594 - INFO - Processed 29500000 reads so far
2011-05-19 16:59:50,334 - INFO - Processed 29600000 reads so far
2011-05-19 17:00:01,372 - INFO - Processed 29700000 reads so far
2011-05-19 17:00:13,810 - INFO - Processed 29800000 reads so far
2011-05-19 17:00:24,626 - INFO - Processed 29900000 reads so far
2011-05-19 17:00:37,349 - INFO - Processed 30000000 reads so far
2011-05-19 17:00:48,838 - INFO - Processed 30100000 reads so far
2011-05-19 17:01:02,807 - INFO - Processed 30200000 reads so far
2011-05-19 17:01:05,503 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:22990018-43010018
2011-05-19 17:01:18,440 - INFO - Processed 30300000 reads so far
2011-05-19 17:01:34,390 - INFO - Processed 30400000 reads so far
2011-05-19 17:01:46,573 - INFO - Processed 30500000 reads so far
2011-05-19 17:01:59,977 - INFO - Processed 30600000 reads so far
2011-05-19 17:02:14,056 - INFO - Processed 30700000 reads so far
2011-05-19 17:02:26,578 - INFO - Processed 30800000 reads so far
2011-05-19 17:02:37,729 - INFO - Processed 30900000 reads so far
2011-05-19 17:02:50,311 - INFO - Processed 31000000 reads so far
2011-05-19 17:03:01,861 - INFO - Processed 31100000 reads so far
2011-05-19 17:03:12,416 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:42990042-63010042
2011-05-19 17:03:13,754 - INFO - Processed 31200000 reads so far
2011-05-19 17:03:29,181 - INFO - Processed 31300000 reads so far
2011-05-19 17:03:44,025 - INFO - Processed 31400000 reads so far
2011-05-19 17:03:58,990 - INFO - Processed 31500000 reads so far
2011-05-19 17:04:10,171 - INFO - Processed 31600000 reads so far
2011-05-19 17:04:19,836 - INFO - Processed 31700000 reads so far
2011-05-19 17:04:29,320 - INFO - Processed 31800000 reads so far
2011-05-19 17:04:39,168 - INFO - Processed 31900000 reads so far
2011-05-19 17:04:50,957 - INFO - Processed 32000000 reads so far
2011-05-19 17:05:03,682 - INFO - Processed 32100000 reads so far
2011-05-19 17:05:07,861 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:62990077-83010077
2011-05-19 17:05:14,755 - INFO - Processed 32200000 reads so far
2011-05-19 17:05:26,068 - INFO - Processed 32300000 reads so far
2011-05-19 17:05:38,486 - INFO - Processed 32400000 reads so far
2011-05-19 17:05:53,660 - INFO - Processed 32500000 reads so far
2011-05-19 17:06:08,971 - INFO - Processed 32600000 reads so far
2011-05-19 17:06:22,041 - INFO - Processed 32700000 reads so far
2011-05-19 17:06:32,656 - INFO - Processed 32800000 reads so far
2011-05-19 17:06:43,698 - INFO - Processed 32900000 reads so far
2011-05-19 17:06:56,304 - INFO - Processed 33000000 reads so far
2011-05-19 17:07:10,023 - INFO - Processed 33100000 reads so far
2011-05-19 17:07:16,325 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:82990121-103010121
2011-05-19 17:07:23,626 - INFO - Processed 33200000 reads so far
2011-05-19 17:07:36,584 - INFO - Processed 33300000 reads so far
2011-05-19 17:07:52,632 - INFO - Processed 33400000 reads so far
2011-05-19 17:08:02,881 - INFO - Processed 33500000 reads so far
2011-05-19 17:08:15,716 - INFO - Processed 33600000 reads so far
2011-05-19 17:08:26,519 - INFO - Processed 33700000 reads so far
2011-05-19 17:08:37,057 - INFO - Processed 33800000 reads so far
2011-05-19 17:08:48,007 - INFO - Processed 33900000 reads so far
2011-05-19 17:08:57,284 - INFO - Processed 34000000 reads so far
2011-05-19 17:09:08,259 - INFO - Processed 34100000 reads so far
2011-05-19 17:09:14,363 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr15:102990160-123010160
2011-05-19 17:09:17,114 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:2990212-23010212
2011-05-19 17:09:21,015 - INFO - Processed 34200000 reads so far
2011-05-19 17:09:32,496 - INFO - Processed 34300000 reads so far
2011-05-19 17:09:43,815 - INFO - Processed 34400000 reads so far
2011-05-19 17:09:57,929 - INFO - Processed 34500000 reads so far
2011-05-19 17:10:11,525 - INFO - Processed 34600000 reads so far
2011-05-19 17:10:23,464 - INFO - Processed 34700000 reads so far
2011-05-19 17:10:34,967 - INFO - Processed 34800000 reads so far
2011-05-19 17:10:45,938 - INFO - Processed 34900000 reads so far
2011-05-19 17:10:59,097 - INFO - Processed 35000000 reads so far
2011-05-19 17:11:10,970 - INFO - Processed 35100000 reads so far
2011-05-19 17:11:19,192 - INFO - Processed 35200000 reads so far
2011-05-19 17:11:19,828 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:22990231-43010231
2011-05-19 17:11:30,611 - INFO - Processed 35300000 reads so far
2011-05-19 17:11:39,405 - INFO - Processed 35400000 reads so far
2011-05-19 17:11:47,518 - INFO - Processed 35500000 reads so far
2011-05-19 17:12:01,347 - INFO - Processed 35600000 reads so far
2011-05-19 17:12:12,756 - INFO - Processed 35700000 reads so far
2011-05-19 17:12:24,954 - INFO - Processed 35800000 reads so far
2011-05-19 17:12:38,562 - INFO - Processed 35900000 reads so far
2011-05-19 17:12:48,101 - INFO - Processed 36000000 reads so far
2011-05-19 17:13:01,343 - INFO - Processed 36100000 reads so far
2011-05-19 17:13:10,022 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:42990260-63010260
2011-05-19 17:13:13,173 - INFO - Processed 36200000 reads so far
2011-05-19 17:13:26,606 - INFO - Processed 36300000 reads so far
2011-05-19 17:13:40,089 - INFO - Processed 36400000 reads so far
2011-05-19 17:13:55,308 - INFO - Processed 36500000 reads so far
2011-05-19 17:14:06,021 - INFO - Processed 36600000 reads so far
2011-05-19 17:14:17,614 - INFO - Processed 36700000 reads so far
2011-05-19 17:14:30,882 - INFO - Processed 36800000 reads so far
2011-05-19 17:14:42,942 - INFO - Processed 36900000 reads so far
2011-05-19 17:14:54,069 - INFO - Processed 37000000 reads so far
2011-05-19 17:15:07,519 - INFO - Processed 37100000 reads so far
2011-05-19 17:15:08,271 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:62990288-83010288
2011-05-19 17:15:20,613 - INFO - Processed 37200000 reads so far
2011-05-19 17:15:33,118 - INFO - Processed 37300000 reads so far
2011-05-19 17:15:44,887 - INFO - Processed 37400000 reads so far
2011-05-19 17:15:56,436 - INFO - Processed 37500000 reads so far
2011-05-19 17:16:07,753 - INFO - Processed 37600000 reads so far
2011-05-19 17:16:19,131 - INFO - Processed 37700000 reads so far
2011-05-19 17:16:36,936 - INFO - Processed 37800000 reads so far
2011-05-19 17:16:49,634 - INFO - Processed 37900000 reads so far
2011-05-19 17:17:02,722 - INFO - Processed 38000000 reads so far
2011-05-19 17:17:03,170 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16:82990302-103010302
2011-05-19 17:17:14,372 - INFO - Processed 38100000 reads so far
2011-05-19 17:17:25,638 - INFO - Processed 38200000 reads so far
2011-05-19 17:17:37,717 - INFO - Processed 38300000 reads so far
2011-05-19 17:17:50,872 - INFO - Processed 38400000 reads so far
2011-05-19 17:18:03,608 - INFO - Processed 38500000 reads so far
2011-05-19 17:18:20,504 - INFO - Processed 38600000 reads so far
2011-05-19 17:18:33,349 - INFO - Processed 38700000 reads so far
2011-05-19 17:18:39,843 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr16_random:0-20010090
2011-05-19 17:18:39,862 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:2990015-23010015
2011-05-19 17:18:46,513 - INFO - Processed 38800000 reads so far
2011-05-19 17:18:58,505 - INFO - Processed 38900000 reads so far
2011-05-19 17:19:09,355 - INFO - Processed 39000000 reads so far
2011-05-19 17:19:25,377 - INFO - Processed 39100000 reads so far
2011-05-19 17:19:37,903 - INFO - Processed 39200000 reads so far
2011-05-19 17:19:49,773 - INFO - Processed 39300000 reads so far
2011-05-19 17:20:02,715 - INFO - Processed 39400000 reads so far
2011-05-19 17:20:14,087 - INFO - Processed 39500000 reads so far
2011-05-19 17:20:26,269 - INFO - Processed 39600000 reads so far
2011-05-19 17:20:42,220 - INFO - Processed 39700000 reads so far
2011-05-19 17:20:50,112 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:22990064-43010064
2011-05-19 17:20:54,058 - INFO - Processed 39800000 reads so far
2011-05-19 17:21:08,966 - INFO - Processed 39900000 reads so far
2011-05-19 17:21:20,973 - INFO - Processed 40000000 reads so far
2011-05-19 17:21:32,848 - INFO - Processed 40100000 reads so far
2011-05-19 17:21:46,324 - INFO - Processed 40200000 reads so far
2011-05-19 17:22:00,243 - INFO - Processed 40300000 reads so far
2011-05-19 17:22:15,675 - INFO - Processed 40400000 reads so far
2011-05-19 17:22:26,833 - INFO - Processed 40500000 reads so far
2011-05-19 17:22:39,365 - INFO - Processed 40600000 reads so far
2011-05-19 17:22:50,994 - INFO - Processed 40700000 reads so far
2011-05-19 17:23:03,040 - INFO - Processed 40800000 reads so far
2011-05-19 17:23:11,348 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:42990077-63010077
2011-05-19 17:23:19,493 - INFO - Processed 40900000 reads so far
2011-05-19 17:23:33,624 - INFO - Processed 41000000 reads so far
2011-05-19 17:23:47,385 - INFO - Processed 41100000 reads so far
2011-05-19 17:24:02,701 - INFO - Processed 41200000 reads so far
2011-05-19 17:24:14,311 - INFO - Processed 41300000 reads so far
2011-05-19 17:24:25,674 - INFO - Processed 41400000 reads so far
2011-05-19 17:24:40,244 - INFO - Processed 41500000 reads so far
2011-05-19 17:24:52,931 - INFO - Processed 41600000 reads so far
2011-05-19 17:25:06,501 - INFO - Processed 41700000 reads so far
2011-05-19 17:25:17,127 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:62990099-83010099
2011-05-19 17:25:19,399 - INFO - Processed 41800000 reads so far
2011-05-19 17:25:33,437 - INFO - Processed 41900000 reads so far
2011-05-19 17:25:48,428 - INFO - Processed 42000000 reads so far
2011-05-19 17:26:02,539 - INFO - Processed 42100000 reads so far
2011-05-19 17:26:13,831 - INFO - Processed 42200000 reads so far
2011-05-19 17:26:26,464 - INFO - Processed 42300000 reads so far
2011-05-19 17:26:37,931 - INFO - Processed 42400000 reads so far
2011-05-19 17:26:50,770 - INFO - Processed 42500000 reads so far
2011-05-19 17:27:05,009 - INFO - Processed 42600000 reads so far
2011-05-19 17:27:17,195 - INFO - Processed 42700000 reads so far
2011-05-19 17:27:21,313 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17:82990134-103010134
2011-05-19 17:27:26,172 - INFO - Processed 42800000 reads so far
2011-05-19 17:27:35,060 - INFO - Processed 42900000 reads so far
2011-05-19 17:27:43,029 - INFO - Processed 43000000 reads so far
2011-05-19 17:27:50,827 - INFO - Processed 43100000 reads so far
2011-05-19 17:27:59,220 - INFO - Processed 43200000 reads so far
2011-05-19 17:28:13,442 - INFO - Processed 43300000 reads so far
2011-05-19 17:28:17,499 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr17_random:0-20010160
2011-05-19 17:28:19,249 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:2990000-23010000
2011-05-19 17:28:25,338 - INFO - Processed 43400000 reads so far
2011-05-19 17:28:38,405 - INFO - Processed 43500000 reads so far
2011-05-19 17:28:50,613 - INFO - Processed 43600000 reads so far
2011-05-19 17:29:02,133 - INFO - Processed 43700000 reads so far
2011-05-19 17:29:15,466 - INFO - Processed 43800000 reads so far
2011-05-19 17:29:28,939 - INFO - Processed 43900000 reads so far
2011-05-19 17:29:40,259 - INFO - Processed 44000000 reads so far
2011-05-19 17:29:55,176 - INFO - Processed 44100000 reads so far
2011-05-19 17:30:07,440 - INFO - Processed 44200000 reads so far
2011-05-19 17:30:21,358 - INFO - Processed 44300000 reads so far
2011-05-19 17:30:26,644 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:22990027-43010027
2011-05-19 17:30:34,952 - INFO - Processed 44400000 reads so far
2011-05-19 17:30:46,566 - INFO - Processed 44500000 reads so far
2011-05-19 17:30:59,162 - INFO - Processed 44600000 reads so far
2011-05-19 17:31:10,399 - INFO - Processed 44700000 reads so far
2011-05-19 17:31:21,853 - INFO - Processed 44800000 reads so far
2011-05-19 17:31:37,884 - INFO - Processed 44900000 reads so far
2011-05-19 17:31:49,532 - INFO - Processed 45000000 reads so far
2011-05-19 17:32:01,194 - INFO - Processed 45100000 reads so far
2011-05-19 17:32:13,978 - INFO - Processed 45200000 reads so far
2011-05-19 17:32:26,740 - INFO - Processed 45300000 reads so far
2011-05-19 17:32:28,984 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:42990072-63010072
2011-05-19 17:32:42,591 - INFO - Processed 45400000 reads so far
2011-05-19 17:32:56,421 - INFO - Processed 45500000 reads so far
2011-05-19 17:33:07,990 - INFO - Processed 45600000 reads so far
2011-05-19 17:33:21,441 - INFO - Processed 45700000 reads so far
2011-05-19 17:33:32,768 - INFO - Processed 45800000 reads so far
2011-05-19 17:33:44,987 - INFO - Processed 45900000 reads so far
2011-05-19 17:33:58,520 - INFO - Processed 46000000 reads so far
2011-05-19 17:34:10,949 - INFO - Processed 46100000 reads so far
2011-05-19 17:34:25,574 - INFO - Processed 46200000 reads so far
2011-05-19 17:34:35,607 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:62990135-83010135
2011-05-19 17:34:38,618 - INFO - Processed 46300000 reads so far
2011-05-19 17:34:51,931 - INFO - Processed 46400000 reads so far
2011-05-19 17:35:04,266 - INFO - Processed 46500000 reads so far
2011-05-19 17:35:14,974 - INFO - Processed 46600000 reads so far
2011-05-19 17:35:24,269 - INFO - Processed 46700000 reads so far
2011-05-19 17:35:36,814 - INFO - Processed 46800000 reads so far
2011-05-19 17:35:47,475 - INFO - Processed 46900000 reads so far
2011-05-19 17:36:00,007 - INFO - Processed 47000000 reads so far
2011-05-19 17:36:14,812 - INFO - Processed 47100000 reads so far
2011-05-19 17:36:26,146 - INFO - Processed 47200000 reads so far
2011-05-19 17:36:33,258 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr18:82990140-103010140
2011-05-19 17:36:37,373 - INFO - Processed 47300000 reads so far
2011-05-19 17:36:48,606 - INFO - Processed 47400000 reads so far
2011-05-19 17:37:01,903 - INFO - Processed 47500000 reads so far
2011-05-19 17:37:12,844 - INFO - Processed 47600000 reads so far
2011-05-19 17:37:16,600 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:2990006-23010006
2011-05-19 17:37:26,081 - INFO - Processed 47700000 reads so far
2011-05-19 17:37:39,475 - INFO - Processed 47800000 reads so far
2011-05-19 17:37:50,622 - INFO - Processed 47900000 reads so far
2011-05-19 17:38:04,325 - INFO - Processed 48000000 reads so far
2011-05-19 17:38:15,909 - INFO - Processed 48100000 reads so far
2011-05-19 17:38:30,935 - INFO - Processed 48200000 reads so far
2011-05-19 17:38:48,882 - INFO - Processed 48300000 reads so far
2011-05-19 17:39:01,650 - INFO - Processed 48400000 reads so far
2011-05-19 17:39:17,350 - INFO - Processed 48500000 reads so far
2011-05-19 17:39:28,481 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:22990050-43010050
2011-05-19 17:39:29,060 - INFO - Processed 48600000 reads so far
2011-05-19 17:39:40,380 - INFO - Processed 48700000 reads so far
2011-05-19 17:39:53,188 - INFO - Processed 48800000 reads so far
2011-05-19 17:40:05,001 - INFO - Processed 48900000 reads so far
2011-05-19 17:40:16,964 - INFO - Processed 49000000 reads so far
2011-05-19 17:40:28,788 - INFO - Processed 49100000 reads so far
2011-05-19 17:40:40,007 - INFO - Processed 49200000 reads so far
2011-05-19 17:40:54,186 - INFO - Processed 49300000 reads so far
2011-05-19 17:41:04,220 - INFO - Processed 49400000 reads so far
2011-05-19 17:41:15,584 - INFO - Processed 49500000 reads so far
2011-05-19 17:41:24,388 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr19:42990095-63010095
2011-05-19 17:41:29,810 - INFO - Processed 49600000 reads so far
2011-05-19 17:41:42,653 - INFO - Processed 49700000 reads so far
2011-05-19 17:41:54,415 - INFO - Processed 49800000 reads so far
2011-05-19 17:42:08,260 - INFO - Processed 49900000 reads so far
2011-05-19 17:42:20,145 - INFO - Processed 50000000 reads so far
2011-05-19 17:42:33,346 - INFO - Processed 50100000 reads so far
2011-05-19 17:42:47,837 - INFO - Processed 50200000 reads so far
2011-05-19 17:43:01,175 - INFO - Processed 50300000 reads so far
2011-05-19 17:43:15,549 - INFO - Processed 50400000 reads so far
2011-05-19 17:43:27,597 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:2989979-23009979
2011-05-19 17:43:30,500 - INFO - Processed 50500000 reads so far
2011-05-19 17:43:42,187 - INFO - Processed 50600000 reads so far
2011-05-19 17:43:52,737 - INFO - Processed 50700000 reads so far
2011-05-19 17:44:05,771 - INFO - Processed 50800000 reads so far
2011-05-19 17:44:18,689 - INFO - Processed 50900000 reads so far
2011-05-19 17:44:30,030 - INFO - Processed 51000000 reads so far
2011-05-19 17:44:38,413 - INFO - Processed 51100000 reads so far
2011-05-19 17:44:49,425 - INFO - Processed 51200000 reads so far
2011-05-19 17:45:00,126 - INFO - Processed 51300000 reads so far
2011-05-19 17:45:11,557 - INFO - Processed 51400000 reads so far
2011-05-19 17:45:14,176 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:22990152-43010152
2011-05-19 17:45:24,320 - INFO - Processed 51500000 reads so far
2011-05-19 17:45:36,015 - INFO - Processed 51600000 reads so far
2011-05-19 17:45:46,258 - INFO - Processed 51700000 reads so far
2011-05-19 17:45:58,102 - INFO - Processed 51800000 reads so far
2011-05-19 17:46:11,039 - INFO - Processed 51900000 reads so far
2011-05-19 17:46:22,557 - INFO - Processed 52000000 reads so far
2011-05-19 17:46:36,373 - INFO - Processed 52100000 reads so far
2011-05-19 17:46:47,343 - INFO - Processed 52200000 reads so far
2011-05-19 17:46:56,729 - INFO - Processed 52300000 reads so far
2011-05-19 17:47:06,135 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:42990164-63010164
2011-05-19 17:47:07,849 - INFO - Processed 52400000 reads so far
2011-05-19 17:47:19,416 - INFO - Processed 52500000 reads so far
2011-05-19 17:47:29,098 - INFO - Processed 52600000 reads so far
2011-05-19 17:47:46,426 - INFO - Processed 52700000 reads so far
2011-05-19 17:47:58,035 - INFO - Processed 52800000 reads so far
2011-05-19 17:48:10,283 - INFO - Processed 52900000 reads so far
2011-05-19 17:48:21,917 - INFO - Processed 53000000 reads so far
2011-05-19 17:48:33,681 - INFO - Processed 53100000 reads so far
2011-05-19 17:48:45,450 - INFO - Processed 53200000 reads so far
2011-05-19 17:48:59,602 - INFO - Processed 53300000 reads so far
2011-05-19 17:49:03,881 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:62990173-83010173
2011-05-19 17:49:12,835 - INFO - Processed 53400000 reads so far
2011-05-19 17:49:25,134 - INFO - Processed 53500000 reads so far
2011-05-19 17:49:33,323 - INFO - Processed 53600000 reads so far
2011-05-19 17:49:43,755 - INFO - Processed 53700000 reads so far
2011-05-19 17:49:56,321 - INFO - Processed 53800000 reads so far
2011-05-19 17:50:12,013 - INFO - Processed 53900000 reads so far
2011-05-19 17:50:23,592 - INFO - Processed 54000000 reads so far
2011-05-19 17:50:37,941 - INFO - Processed 54100000 reads so far
2011-05-19 17:50:50,692 - INFO - Processed 54200000 reads so far
2011-05-19 17:51:01,052 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:82990183-103010183
2011-05-19 17:51:02,458 - INFO - Processed 54300000 reads so far
2011-05-19 17:51:16,176 - INFO - Processed 54400000 reads so far
2011-05-19 17:51:25,947 - INFO - Processed 54500000 reads so far
2011-05-19 17:51:36,712 - INFO - Processed 54600000 reads so far
2011-05-19 17:51:45,229 - INFO - Processed 54700000 reads so far
2011-05-19 17:51:57,547 - INFO - Processed 54800000 reads so far
2011-05-19 17:52:05,396 - INFO - Processed 54900000 reads so far
2011-05-19 17:52:13,808 - INFO - Processed 55000000 reads so far
2011-05-19 17:52:26,534 - INFO - Processed 55100000 reads so far
2011-05-19 17:52:40,506 - INFO - Processed 55200000 reads so far
2011-05-19 17:52:46,689 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:102990184-123010184
2011-05-19 17:52:53,072 - INFO - Processed 55300000 reads so far
2011-05-19 17:53:06,689 - INFO - Processed 55400000 reads so far
2011-05-19 17:53:15,566 - INFO - Processed 55500000 reads so far
2011-05-19 17:53:22,962 - INFO - Processed 55600000 reads so far
2011-05-19 17:53:34,472 - INFO - Processed 55700000 reads so far
2011-05-19 17:53:42,679 - INFO - Processed 55800000 reads so far
2011-05-19 17:53:53,763 - INFO - Processed 55900000 reads so far
2011-05-19 17:54:02,687 - INFO - Processed 56000000 reads so far
2011-05-19 17:54:11,414 - INFO - Processed 56100000 reads so far
2011-05-19 17:54:24,820 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:122990270-143010270
2011-05-19 17:54:26,171 - INFO - Processed 56200000 reads so far
2011-05-19 17:54:40,245 - INFO - Processed 56300000 reads so far
2011-05-19 17:54:53,148 - INFO - Processed 56400000 reads so far
2011-05-19 17:55:03,668 - INFO - Processed 56500000 reads so far
2011-05-19 17:55:13,142 - INFO - Processed 56600000 reads so far
2011-05-19 17:55:25,948 - INFO - Processed 56700000 reads so far
2011-05-19 17:55:36,759 - INFO - Processed 56800000 reads so far
2011-05-19 17:55:49,567 - INFO - Processed 56900000 reads so far
2011-05-19 17:56:00,701 - INFO - Processed 57000000 reads so far
2011-05-19 17:56:14,899 - INFO - Processed 57100000 reads so far
2011-05-19 17:56:25,328 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:142990331-163010331
2011-05-19 17:56:29,844 - INFO - Processed 57200000 reads so far
2011-05-19 17:56:42,549 - INFO - Processed 57300000 reads so far
2011-05-19 17:56:56,658 - INFO - Processed 57400000 reads so far
2011-05-19 17:57:07,625 - INFO - Processed 57500000 reads so far
2011-05-19 17:57:16,122 - INFO - Processed 57600000 reads so far
2011-05-19 17:57:28,796 - INFO - Processed 57700000 reads so far
2011-05-19 17:57:40,340 - INFO - Processed 57800000 reads so far
2011-05-19 17:57:51,813 - INFO - Processed 57900000 reads so far
2011-05-19 17:58:03,179 - INFO - Processed 58000000 reads so far
2011-05-19 17:58:15,371 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:162990341-183010341
2011-05-19 17:58:16,354 - INFO - Processed 58100000 reads so far
2011-05-19 17:58:28,167 - INFO - Processed 58200000 reads so far
2011-05-19 17:58:41,275 - INFO - Processed 58300000 reads so far
2011-05-19 17:58:52,613 - INFO - Processed 58400000 reads so far
2011-05-19 17:59:04,031 - INFO - Processed 58500000 reads so far
2011-05-19 17:59:17,196 - INFO - Processed 58600000 reads so far
2011-05-19 17:59:31,960 - INFO - Processed 58700000 reads so far
2011-05-19 17:59:44,784 - INFO - Processed 58800000 reads so far
2011-05-19 17:59:58,306 - INFO - Processed 58900000 reads so far
2011-05-19 18:00:09,646 - INFO - Processed 59000000 reads so far
2011-05-19 18:00:21,309 - INFO - Processed 59100000 reads so far
2011-05-19 18:00:21,946 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1:182990351-203010351
2011-05-19 18:00:32,796 - INFO - Processed 59200000 reads so far
2011-05-19 18:00:44,413 - INFO - Processed 59300000 reads so far
2011-05-19 18:00:56,513 - INFO - Processed 59400000 reads so far
2011-05-19 18:01:10,739 - INFO - Processed 59500000 reads so far
2011-05-19 18:01:22,100 - INFO - Processed 59600000 reads so far
2011-05-19 18:01:33,813 - INFO - Processed 59700000 reads so far
2011-05-19 18:01:44,749 - INFO - Processed 59800000 reads so far
2011-05-19 18:01:45,380 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr1_random:0-20010000
2011-05-19 18:01:56,444 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:2990003-23010003
2011-05-19 18:01:57,573 - INFO - Processed 59900000 reads so far
2011-05-19 18:02:11,046 - INFO - Processed 60000000 reads so far
2011-05-19 18:02:22,352 - INFO - Processed 60100000 reads so far
2011-05-19 18:02:33,031 - INFO - Processed 60200000 reads so far
2011-05-19 18:02:43,999 - INFO - Processed 60300000 reads so far
2011-05-19 18:02:55,192 - INFO - Processed 60400000 reads so far
2011-05-19 18:03:06,276 - INFO - Processed 60500000 reads so far
2011-05-19 18:03:18,187 - INFO - Processed 60600000 reads so far
2011-05-19 18:03:29,397 - INFO - Processed 60700000 reads so far
2011-05-19 18:03:38,341 - INFO - Processed 60800000 reads so far
2011-05-19 18:03:45,513 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:22990005-43010005
2011-05-19 18:03:48,125 - INFO - Processed 60900000 reads so far
2011-05-19 18:03:59,626 - INFO - Processed 61000000 reads so far
2011-05-19 18:04:08,376 - INFO - Processed 61100000 reads so far
2011-05-19 18:04:24,786 - INFO - Processed 61200000 reads so far
2011-05-19 18:04:37,745 - INFO - Processed 61300000 reads so far
2011-05-19 18:04:48,404 - INFO - Processed 61400000 reads so far
2011-05-19 18:05:01,461 - INFO - Processed 61500000 reads so far
2011-05-19 18:05:11,334 - INFO - Processed 61600000 reads so far
2011-05-19 18:05:21,490 - INFO - Processed 61700000 reads so far
2011-05-19 18:05:34,386 - INFO - Processed 61800000 reads so far
2011-05-19 18:05:41,812 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:42990008-63010008
2011-05-19 18:05:47,927 - INFO - Processed 61900000 reads so far
2011-05-19 18:06:00,045 - INFO - Processed 62000000 reads so far
2011-05-19 18:06:13,082 - INFO - Processed 62100000 reads so far
2011-05-19 18:06:24,453 - INFO - Processed 62200000 reads so far
2011-05-19 18:06:41,148 - INFO - Processed 62300000 reads so far
2011-05-19 18:06:52,533 - INFO - Processed 62400000 reads so far
2011-05-19 18:07:03,832 - INFO - Processed 62500000 reads so far
2011-05-19 18:07:15,818 - INFO - Processed 62600000 reads so far
2011-05-19 18:07:27,807 - INFO - Processed 62700000 reads so far
2011-05-19 18:07:38,547 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:62990105-83010105
2011-05-19 18:07:39,687 - INFO - Processed 62800000 reads so far
2011-05-19 18:07:53,282 - INFO - Processed 62900000 reads so far
2011-05-19 18:08:03,547 - INFO - Processed 63000000 reads so far
2011-05-19 18:08:12,613 - INFO - Processed 63100000 reads so far
2011-05-19 18:08:23,938 - INFO - Processed 63200000 reads so far
2011-05-19 18:08:34,509 - INFO - Processed 63300000 reads so far
2011-05-19 18:08:46,815 - INFO - Processed 63400000 reads so far
2011-05-19 18:08:57,895 - INFO - Processed 63500000 reads so far
2011-05-19 18:09:08,283 - INFO - Processed 63600000 reads so far
2011-05-19 18:09:18,258 - INFO - Processed 63700000 reads so far
2011-05-19 18:09:24,017 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:82990110-103010110
2011-05-19 18:09:31,621 - INFO - Processed 63800000 reads so far
2011-05-19 18:09:45,175 - INFO - Processed 63900000 reads so far
2011-05-19 18:09:57,371 - INFO - Processed 64000000 reads so far
2011-05-19 18:10:10,061 - INFO - Processed 64100000 reads so far
2011-05-19 18:10:23,555 - INFO - Processed 64200000 reads so far
2011-05-19 18:10:31,795 - INFO - Processed 64300000 reads so far
2011-05-19 18:10:42,065 - INFO - Processed 64400000 reads so far
2011-05-19 18:10:51,297 - INFO - Processed 64500000 reads so far
2011-05-19 18:11:00,510 - INFO - Processed 64600000 reads so far
2011-05-19 18:11:10,799 - INFO - Processed 64700000 reads so far
2011-05-19 18:11:19,961 - INFO - Processed 64800000 reads so far
2011-05-19 18:11:33,434 - INFO - Processed 64900000 reads so far
2011-05-19 18:11:41,716 - INFO - Processed 65000000 reads so far
2011-05-19 18:11:49,311 - INFO - Processed 65100000 reads so far
2011-05-19 18:11:56,421 - INFO - Processed 65200000 reads so far
2011-05-19 18:12:04,990 - INFO - Processed 65300000 reads so far
2011-05-19 18:12:11,794 - INFO - Processed 65400000 reads so far
2011-05-19 18:12:20,113 - INFO - Processed 65500000 reads so far
2011-05-19 18:12:27,966 - INFO - Processed 65600000 reads so far
2011-05-19 18:12:36,524 - INFO - Processed 65700000 reads so far
2011-05-19 18:12:48,661 - INFO - Processed 65800000 reads so far
2011-05-19 18:12:55,462 - INFO - Processed 65900000 reads so far
2011-05-19 18:13:03,946 - INFO - Processed 66000000 reads so far
2011-05-19 18:13:11,630 - INFO - Processed 66100000 reads so far
2011-05-19 18:13:21,378 - INFO - Processed 66200000 reads so far
2011-05-19 18:13:30,057 - INFO - Processed 66300000 reads so far
2011-05-19 18:13:38,921 - INFO - Processed 66400000 reads so far
2011-05-19 18:13:44,446 - INFO - Processed 66500000 reads so far
2011-05-19 18:13:51,708 - INFO - Processed 66600000 reads so far
2011-05-19 18:14:01,109 - INFO - Processed 66700000 reads so far
2011-05-19 18:14:09,495 - INFO - Processed 66800000 reads so far
2011-05-19 18:14:18,362 - INFO - Processed 66900000 reads so far
2011-05-19 18:14:26,666 - INFO - Processed 67000000 reads so far
2011-05-19 18:14:36,632 - INFO - Processed 67100000 reads so far
2011-05-19 18:14:43,841 - INFO - Processed 67200000 reads so far
2011-05-19 18:14:51,493 - INFO - Processed 67300000 reads so far
2011-05-19 18:14:57,557 - INFO - Processed 67400000 reads so far
2011-05-19 18:15:04,679 - INFO - Processed 67500000 reads so far
2011-05-19 18:15:11,709 - INFO - Processed 67600000 reads so far
2011-05-19 18:15:18,922 - INFO - Processed 67700000 reads so far
2011-05-19 18:15:26,534 - INFO - Processed 67800000 reads so far
2011-05-19 18:15:34,083 - INFO - Processed 67900000 reads so far
2011-05-19 18:15:40,243 - INFO - Processed 68000000 reads so far
2011-05-19 18:15:48,819 - INFO - Processed 68100000 reads so far
2011-05-19 18:15:56,147 - INFO - Processed 68200000 reads so far
2011-05-19 18:16:05,432 - INFO - Processed 68300000 reads so far
2011-05-19 18:16:12,700 - INFO - Processed 68400000 reads so far
2011-05-19 18:16:21,316 - INFO - Processed 68500000 reads so far
2011-05-19 18:16:32,963 - INFO - Processed 68600000 reads so far
2011-05-19 18:16:41,653 - INFO - Processed 68700000 reads so far
2011-05-19 18:16:50,006 - INFO - Processed 68800000 reads so far
2011-05-19 18:16:59,636 - INFO - Processed 68900000 reads so far
2011-05-19 18:17:11,846 - INFO - Processed 69000000 reads so far
2011-05-19 18:17:21,069 - INFO - Processed 69100000 reads so far
2011-05-19 18:17:31,502 - INFO - Processed 69200000 reads so far
2011-05-19 18:17:41,680 - INFO - Processed 69300000 reads so far
2011-05-19 18:17:50,285 - INFO - Processed 69400000 reads so far
2011-05-19 18:17:57,393 - INFO - Processed 69500000 reads so far
2011-05-19 18:18:06,481 - INFO - Processed 69600000 reads so far
2011-05-19 18:24:14,662 - INFO - Processed 69700000 reads so far
2011-05-19 18:24:20,786 - INFO - Processed 69800000 reads so far
2011-05-19 18:24:27,094 - INFO - Processed 69900000 reads so far
2011-05-19 18:24:32,959 - INFO - Processed 70000000 reads so far
2011-05-19 18:24:42,144 - INFO - Processed 70100000 reads so far
2011-05-19 18:24:53,297 - INFO - Processed 70200000 reads so far
2011-05-19 18:25:05,365 - INFO - Processed 70300000 reads so far
2011-05-19 18:25:14,985 - INFO - Processed 70400000 reads so far
2011-05-19 18:25:23,514 - INFO - Processed 70500000 reads so far
2011-05-19 18:25:32,219 - INFO - Processed 70600000 reads so far
2011-05-19 18:25:40,383 - INFO - Processed 70700000 reads so far
2011-05-19 18:25:48,259 - INFO - Processed 70800000 reads so far
2011-05-19 18:25:56,225 - INFO - Processed 70900000 reads so far
2011-05-19 18:26:03,822 - INFO - Processed 71000000 reads so far
2011-05-19 18:26:10,760 - INFO - Processed 71100000 reads so far
2011-05-19 18:26:18,598 - INFO - Processed 71200000 reads so far
2011-05-19 18:26:27,123 - INFO - Processed 71300000 reads so far
2011-05-19 18:26:34,191 - INFO - Processed 71400000 reads so far
2011-05-19 18:26:41,719 - INFO - Processed 71500000 reads so far
2011-05-19 18:26:49,915 - INFO - Processed 71600000 reads so far
2011-05-19 18:26:56,883 - INFO - Processed 71700000 reads so far
2011-05-19 18:27:05,959 - INFO - Processed 71800000 reads so far
2011-05-19 18:27:14,360 - INFO - Processed 71900000 reads so far
2011-05-19 18:27:23,382 - INFO - Processed 72000000 reads so far
2011-05-19 18:27:32,902 - INFO - Processed 72100000 reads so far
2011-05-19 18:27:41,681 - INFO - Processed 72200000 reads so far
2011-05-19 18:27:51,092 - INFO - Processed 72300000 reads so far
2011-05-19 18:28:00,883 - INFO - Processed 72400000 reads so far
2011-05-19 18:28:10,243 - INFO - Processed 72500000 reads so far
2011-05-19 18:28:19,233 - INFO - Processed 72600000 reads so far
2011-05-19 18:28:29,207 - INFO - Processed 72700000 reads so far
2011-05-19 18:28:39,036 - INFO - Processed 72800000 reads so far
2011-05-19 18:28:49,023 - INFO - Processed 72900000 reads so far
2011-05-19 18:28:57,733 - INFO - Processed 73000000 reads so far
2011-05-19 18:29:08,720 - INFO - Processed 73100000 reads so far
2011-05-19 18:29:17,565 - INFO - Processed 73200000 reads so far
2011-05-19 18:29:23,339 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:102990126-123010126
2011-05-19 18:29:30,318 - INFO - Processed 73300000 reads so far
2011-05-19 18:29:39,469 - INFO - Processed 73400000 reads so far
2011-05-19 18:29:49,178 - INFO - Processed 73500000 reads so far
2011-05-19 18:29:59,374 - INFO - Processed 73600000 reads so far
2011-05-19 18:30:10,937 - INFO - Processed 73700000 reads so far
2011-05-19 18:30:22,759 - INFO - Processed 73800000 reads so far
2011-05-19 18:30:34,307 - INFO - Processed 73900000 reads so far
2011-05-19 18:30:45,760 - INFO - Processed 74000000 reads so far
2011-05-19 18:30:54,884 - INFO - Processed 74100000 reads so far
2011-05-19 18:31:05,619 - INFO - Processed 74200000 reads so far
2011-05-19 18:31:07,632 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:122990175-143010175
2011-05-19 18:31:18,306 - INFO - Processed 74300000 reads so far
2011-05-19 18:31:32,571 - INFO - Processed 74400000 reads so far
2011-05-19 18:31:43,734 - INFO - Processed 74500000 reads so far
2011-05-19 18:31:56,751 - INFO - Processed 74600000 reads so far
2011-05-19 18:32:09,298 - INFO - Processed 74700000 reads so far
2011-05-19 18:32:19,400 - INFO - Processed 74800000 reads so far
2011-05-19 18:32:29,105 - INFO - Processed 74900000 reads so far
2011-05-19 18:32:40,294 - INFO - Processed 75000000 reads so far
2011-05-19 18:32:50,070 - INFO - Processed 75100000 reads so far
2011-05-19 18:33:01,989 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:142990203-163010203
2011-05-19 18:33:02,418 - INFO - Processed 75200000 reads so far
2011-05-19 18:33:13,457 - INFO - Processed 75300000 reads so far
2011-05-19 18:33:23,682 - INFO - Processed 75400000 reads so far
2011-05-19 18:33:37,152 - INFO - Processed 75500000 reads so far
2011-05-19 18:33:47,199 - INFO - Processed 75600000 reads so far
2011-05-19 18:33:57,713 - INFO - Processed 75700000 reads so far
2011-05-19 18:34:12,402 - INFO - Processed 75800000 reads so far
2011-05-19 18:34:22,839 - INFO - Processed 75900000 reads so far
2011-05-19 18:34:34,987 - INFO - Processed 76000000 reads so far
2011-05-19 18:34:49,118 - INFO - Processed 76100000 reads so far
2011-05-19 18:34:59,553 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr2:162990221-183010221
2011-05-19 18:35:00,826 - INFO - Processed 76200000 reads so far
2011-05-19 18:35:12,010 - INFO - Processed 76300000 reads so far
2011-05-19 18:35:24,245 - INFO - Processed 76400000 reads so far
2011-05-19 18:35:34,235 - INFO - Processed 76500000 reads so far
2011-05-19 18:35:43,915 - INFO - Processed 76600000 reads so far
2011-05-19 18:35:56,336 - INFO - Processed 76700000 reads so far
2011-05-19 18:36:08,534 - INFO - Processed 76800000 reads so far
2011-05-19 18:36:21,257 - INFO - Processed 76900000 reads so far
2011-05-19 18:36:39,285 - INFO - Processed 77000000 reads so far
2011-05-19 18:36:51,020 - INFO - Processed 77100000 reads so far
2011-05-19 18:36:59,040 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:2989993-23009993
2011-05-19 18:37:01,366 - INFO - Processed 77200000 reads so far
2011-05-19 18:37:14,511 - INFO - Processed 77300000 reads so far
2011-05-19 18:37:26,493 - INFO - Processed 77400000 reads so far
2011-05-19 18:37:38,833 - INFO - Processed 77500000 reads so far
2011-05-19 18:37:48,046 - INFO - Processed 77600000 reads so far
2011-05-19 18:38:00,671 - INFO - Processed 77700000 reads so far
2011-05-19 18:38:11,480 - INFO - Processed 77800000 reads so far
2011-05-19 18:38:24,570 - INFO - Processed 77900000 reads so far
2011-05-19 18:38:35,905 - INFO - Processed 78000000 reads so far
2011-05-19 18:38:50,304 - INFO - Processed 78100000 reads so far
2011-05-19 18:38:54,257 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:22990046-43010046
2011-05-19 18:39:00,435 - INFO - Processed 78200000 reads so far
2011-05-19 18:39:13,453 - INFO - Processed 78300000 reads so far
2011-05-19 18:39:26,998 - INFO - Processed 78400000 reads so far
2011-05-19 18:39:36,836 - INFO - Processed 78500000 reads so far
2011-05-19 18:39:48,223 - INFO - Processed 78600000 reads so far
2011-05-19 18:39:58,831 - INFO - Processed 78700000 reads so far
2011-05-19 18:40:09,406 - INFO - Processed 78800000 reads so far
2011-05-19 18:40:19,207 - INFO - Processed 78900000 reads so far
2011-05-19 18:40:29,133 - INFO - Processed 79000000 reads so far
2011-05-19 18:40:40,666 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:42990068-63010068
2011-05-19 18:40:41,506 - INFO - Processed 79100000 reads so far
2011-05-19 18:40:51,996 - INFO - Processed 79200000 reads so far
2011-05-19 18:41:01,823 - INFO - Processed 79300000 reads so far
2011-05-19 18:41:16,823 - INFO - Processed 79400000 reads so far
2011-05-19 18:41:26,738 - INFO - Processed 79500000 reads so far
2011-05-19 18:41:37,028 - INFO - Processed 79600000 reads so far
2011-05-19 18:41:48,130 - INFO - Processed 79700000 reads so far
2011-05-19 18:41:57,167 - INFO - Processed 79800000 reads so far
2011-05-19 18:42:08,442 - INFO - Processed 79900000 reads so far
2011-05-19 18:42:20,700 - INFO - Processed 80000000 reads so far
2011-05-19 18:42:22,160 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:62990085-83010085
2011-05-19 18:42:30,037 - INFO - Processed 80100000 reads so far
2011-05-19 18:42:39,845 - INFO - Processed 80200000 reads so far
2011-05-19 18:42:49,778 - INFO - Processed 80300000 reads so far
2011-05-19 18:43:00,938 - INFO - Processed 80400000 reads so far
2011-05-19 18:43:10,983 - INFO - Processed 80500000 reads so far
2011-05-19 18:43:22,057 - INFO - Processed 80600000 reads so far
2011-05-19 18:43:32,532 - INFO - Processed 80700000 reads so far
2011-05-19 18:43:42,626 - INFO - Processed 80800000 reads so far
2011-05-19 18:43:54,916 - INFO - Processed 80900000 reads so far
2011-05-19 18:44:00,450 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:82990134-103010134
2011-05-19 18:44:07,902 - INFO - Processed 81000000 reads so far
2011-05-19 18:44:16,848 - INFO - Processed 81100000 reads so far
2011-05-19 18:44:28,004 - INFO - Processed 81200000 reads so far
2011-05-19 18:44:40,311 - INFO - Processed 81300000 reads so far
2011-05-19 18:44:52,112 - INFO - Processed 81400000 reads so far
2011-05-19 18:45:03,316 - INFO - Processed 81500000 reads so far
2011-05-19 18:45:16,046 - INFO - Processed 81600000 reads so far
2011-05-19 18:45:27,942 - INFO - Processed 81700000 reads so far
2011-05-19 18:45:38,996 - INFO - Processed 81800000 reads so far
2011-05-19 18:45:50,661 - INFO - Processed 81900000 reads so far
2011-05-19 18:45:52,978 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:102990149-123010149
2011-05-19 18:46:02,545 - INFO - Processed 82000000 reads so far
2011-05-19 18:46:11,206 - INFO - Processed 82100000 reads so far
2011-05-19 18:46:21,162 - INFO - Processed 82200000 reads so far
2011-05-19 18:46:36,423 - INFO - Processed 82300000 reads so far
2011-05-19 18:46:47,847 - INFO - Processed 82400000 reads so far
2011-05-19 18:47:01,470 - INFO - Processed 82500000 reads so far
2011-05-19 18:47:12,462 - INFO - Processed 82600000 reads so far
2011-05-19 18:47:24,097 - INFO - Processed 82700000 reads so far
2011-05-19 18:47:33,711 - INFO - Processed 82800000 reads so far
2011-05-19 18:47:46,258 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:122990200-143010200
2011-05-19 18:47:46,522 - INFO - Processed 82900000 reads so far
2011-05-19 18:47:58,115 - INFO - Processed 83000000 reads so far
2011-05-19 18:48:09,721 - INFO - Processed 83100000 reads so far
2011-05-19 18:48:20,776 - INFO - Processed 83200000 reads so far
2011-05-19 18:48:28,779 - INFO - Processed 83300000 reads so far
2011-05-19 18:48:37,608 - INFO - Processed 83400000 reads so far
2011-05-19 18:48:48,169 - INFO - Processed 83500000 reads so far
2011-05-19 18:48:58,481 - INFO - Processed 83600000 reads so far
2011-05-19 18:49:10,569 - INFO - Processed 83700000 reads so far
2011-05-19 18:49:22,070 - INFO - Processed 83800000 reads so far
2011-05-19 18:49:29,681 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3:142990206-163010206
2011-05-19 18:49:35,694 - INFO - Processed 83900000 reads so far
2011-05-19 18:49:51,067 - INFO - Processed 84000000 reads so far
2011-05-19 18:50:06,398 - INFO - Processed 84100000 reads so far
2011-05-19 18:50:18,097 - INFO - Processed 84200000 reads so far
2011-05-19 18:50:31,362 - INFO - Processed 84300000 reads so far
2011-05-19 18:50:42,457 - INFO - Processed 84400000 reads so far
2011-05-19 18:50:53,596 - INFO - Processed 84500000 reads so far
2011-05-19 18:51:05,716 - INFO - Processed 84600000 reads so far
2011-05-19 18:51:10,752 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr3_random:0-20010028
2011-05-19 18:51:10,880 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:2989977-23009977
2011-05-19 18:51:14,361 - INFO - Processed 84700000 reads so far
2011-05-19 18:51:21,937 - INFO - Processed 84800000 reads so far
2011-05-19 18:51:29,377 - INFO - Processed 84900000 reads so far
2011-05-19 18:51:41,016 - INFO - Processed 85000000 reads so far
2011-05-19 18:51:48,553 - INFO - Processed 85100000 reads so far
2011-05-19 18:52:00,473 - INFO - Processed 85200000 reads so far
2011-05-19 18:52:11,734 - INFO - Processed 85300000 reads so far
2011-05-19 18:52:26,207 - INFO - Processed 85400000 reads so far
2011-05-19 18:52:38,355 - INFO - Processed 85500000 reads so far
2011-05-19 18:52:51,130 - INFO - Processed 85600000 reads so far
2011-05-19 18:52:55,395 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:22989996-43009996
2011-05-19 18:53:01,729 - INFO - Processed 85700000 reads so far
2011-05-19 18:53:09,170 - INFO - Processed 85800000 reads so far
2011-05-19 18:53:18,030 - INFO - Processed 85900000 reads so far
2011-05-19 18:53:31,543 - INFO - Processed 86000000 reads so far
2011-05-19 18:53:46,382 - INFO - Processed 86100000 reads so far
2011-05-19 18:53:56,169 - INFO - Processed 86200000 reads so far
2011-05-19 18:54:04,556 - INFO - Processed 86300000 reads so far
2011-05-19 18:54:13,706 - INFO - Processed 86400000 reads so far
2011-05-19 18:54:59,586 - INFO - Processed 86500000 reads so far
2011-05-19 18:55:03,541 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:42990008-63010008
2011-05-19 18:55:10,784 - INFO - Processed 86600000 reads so far
2011-05-19 18:55:21,696 - INFO - Processed 86700000 reads so far
2011-05-19 18:55:35,541 - INFO - Processed 86800000 reads so far
2011-05-19 18:55:48,317 - INFO - Processed 86900000 reads so far
2011-05-19 18:56:01,985 - INFO - Processed 87000000 reads so far
2011-05-19 18:56:13,588 - INFO - Processed 87100000 reads so far
2011-05-19 18:56:27,630 - INFO - Processed 87200000 reads so far
2011-05-19 18:56:40,866 - INFO - Processed 87300000 reads so far
2011-05-19 18:56:54,592 - INFO - Processed 87400000 reads so far
2011-05-19 18:57:03,616 - INFO - Processed 87500000 reads so far
2011-05-19 18:57:04,528 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:62990040-83010040
2011-05-19 18:57:14,746 - INFO - Processed 87600000 reads so far
2011-05-19 18:57:23,455 - INFO - Processed 87700000 reads so far
2011-05-19 18:57:32,635 - INFO - Processed 87800000 reads so far
2011-05-19 18:57:41,326 - INFO - Processed 87900000 reads so far
2011-05-19 18:57:52,591 - INFO - Processed 88000000 reads so far
2011-05-19 18:58:00,907 - INFO - Processed 88100000 reads so far
2011-05-19 18:58:09,842 - INFO - Processed 88200000 reads so far
2011-05-19 18:58:20,379 - INFO - Processed 88300000 reads so far
2011-05-19 18:58:32,706 - INFO - Processed 88400000 reads so far
2011-05-19 18:58:38,847 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:82990063-103010063
2011-05-19 18:58:44,489 - INFO - Processed 88500000 reads so far
2011-05-19 18:58:55,920 - INFO - Processed 88600000 reads so far
2011-05-19 18:59:08,679 - INFO - Processed 88700000 reads so far
2011-05-19 18:59:19,959 - INFO - Processed 88800000 reads so far
2011-05-19 18:59:30,956 - INFO - Processed 88900000 reads so far
2011-05-19 18:59:40,905 - INFO - Processed 89000000 reads so far
2011-05-19 18:59:51,019 - INFO - Processed 89100000 reads so far
2011-05-19 19:00:00,820 - INFO - Processed 89200000 reads so far
2011-05-19 19:00:10,398 - INFO - Processed 89300000 reads so far
2011-05-19 19:00:20,744 - INFO - Processed 89400000 reads so far
2011-05-19 19:00:23,189 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:102990072-123010072
2011-05-19 19:00:32,424 - INFO - Processed 89500000 reads so far
2011-05-19 19:00:41,888 - INFO - Processed 89600000 reads so far
2011-05-19 19:00:53,370 - INFO - Processed 89700000 reads so far
2011-05-19 19:01:04,885 - INFO - Processed 89800000 reads so far
2011-05-19 19:01:17,591 - INFO - Processed 89900000 reads so far
2011-05-19 19:01:27,327 - INFO - Processed 90000000 reads so far
2011-05-19 19:01:40,252 - INFO - Processed 90100000 reads so far
2011-05-19 19:01:49,910 - INFO - Processed 90200000 reads so far
2011-05-19 19:01:58,717 - INFO - Processed 90300000 reads so far
2011-05-19 19:02:06,665 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:122990084-143010084
2011-05-19 19:02:08,356 - INFO - Processed 90400000 reads so far
2011-05-19 19:02:19,584 - INFO - Processed 90500000 reads so far
2011-05-19 19:02:29,084 - INFO - Processed 90600000 reads so far
2011-05-19 19:02:38,359 - INFO - Processed 90700000 reads so far
2011-05-19 19:02:48,875 - INFO - Processed 90800000 reads so far
2011-05-19 19:02:58,952 - INFO - Processed 90900000 reads so far
2011-05-19 19:03:10,278 - INFO - Processed 91000000 reads so far
2011-05-19 19:03:18,695 - INFO - Processed 91100000 reads so far
2011-05-19 19:03:28,981 - INFO - Processed 91200000 reads so far
2011-05-19 19:03:38,896 - INFO - Processed 91300000 reads so far
2011-05-19 19:03:45,725 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4:142990113-163010113
2011-05-19 19:03:49,953 - INFO - Processed 91400000 reads so far
2011-05-19 19:04:01,210 - INFO - Processed 91500000 reads so far
2011-05-19 19:04:12,518 - INFO - Processed 91600000 reads so far
2011-05-19 19:04:23,711 - INFO - Processed 91700000 reads so far
2011-05-19 19:04:35,219 - INFO - Processed 91800000 reads so far
2011-05-19 19:04:47,324 - INFO - Processed 91900000 reads so far
2011-05-19 19:05:00,106 - INFO - Processed 92000000 reads so far
2011-05-19 19:05:08,085 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr4_random:0-20010047
2011-05-19 19:05:08,976 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:2990090-23010090
2011-05-19 19:05:12,444 - INFO - Processed 92100000 reads so far
2011-05-19 19:05:25,852 - INFO - Processed 92200000 reads so far
2011-05-19 19:05:36,728 - INFO - Processed 92300000 reads so far
2011-05-19 19:05:45,880 - INFO - Processed 92400000 reads so far
2011-05-19 19:05:54,918 - INFO - Processed 92500000 reads so far
2011-05-19 19:06:05,211 - INFO - Processed 92600000 reads so far
2011-05-19 19:06:14,772 - INFO - Processed 92700000 reads so far
2011-05-19 19:06:28,820 - INFO - Processed 92800000 reads so far
2011-05-19 19:06:38,073 - INFO - Processed 92900000 reads so far
2011-05-19 19:06:49,409 - INFO - Processed 93000000 reads so far
2011-05-19 19:06:56,122 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:22990545-43010545
2011-05-19 19:07:01,903 - INFO - Processed 93100000 reads so far
2011-05-19 19:07:13,984 - INFO - Processed 93200000 reads so far
2011-05-19 19:07:22,810 - INFO - Processed 93300000 reads so far
2011-05-19 19:07:32,014 - INFO - Processed 93400000 reads so far
2011-05-19 19:07:45,024 - INFO - Processed 93500000 reads so far
2011-05-19 19:07:58,178 - INFO - Processed 93600000 reads so far
2011-05-19 19:08:11,603 - INFO - Processed 93700000 reads so far
2011-05-19 19:08:23,427 - INFO - Processed 93800000 reads so far
2011-05-19 19:08:34,670 - INFO - Processed 93900000 reads so far
2011-05-19 19:08:45,711 - INFO - Processed 94000000 reads so far
2011-05-19 19:08:48,588 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:42990563-63010563
2011-05-19 19:08:55,169 - INFO - Processed 94100000 reads so far
2011-05-19 19:09:03,598 - INFO - Processed 94200000 reads so far
2011-05-19 19:09:12,589 - INFO - Processed 94300000 reads so far
2011-05-19 19:09:23,170 - INFO - Processed 94400000 reads so far
2011-05-19 19:09:32,843 - INFO - Processed 94500000 reads so far
2011-05-19 19:09:42,623 - INFO - Processed 94600000 reads so far
2011-05-19 19:09:52,133 - INFO - Processed 94700000 reads so far
2011-05-19 19:10:03,541 - INFO - Processed 94800000 reads so far
2011-05-19 19:10:12,851 - INFO - Processed 94900000 reads so far
2011-05-19 19:10:48,048 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:62990570-83010570
2011-05-19 19:10:56,115 - INFO - Processed 95000000 reads so far
2011-05-19 19:11:35,575 - INFO - Processed 95100000 reads so far
2011-05-19 19:11:52,590 - INFO - Processed 95200000 reads so far
2011-05-19 19:12:05,832 - INFO - Processed 95300000 reads so far
2011-05-19 19:12:21,647 - INFO - Processed 95400000 reads so far
2011-05-19 19:12:32,871 - INFO - Processed 95500000 reads so far
2011-05-19 19:12:43,579 - INFO - Processed 95600000 reads so far
2011-05-19 19:12:54,443 - INFO - Processed 95700000 reads so far
2011-05-19 19:13:05,646 - INFO - Processed 95800000 reads so far
2011-05-19 19:13:14,763 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:82990575-103010575
2011-05-19 19:13:15,112 - INFO - Processed 95900000 reads so far
2011-05-19 19:13:23,806 - INFO - Processed 96000000 reads so far
2011-05-19 19:13:34,016 - INFO - Processed 96100000 reads so far
2011-05-19 19:13:45,859 - INFO - Processed 96200000 reads so far
2011-05-19 19:13:58,141 - INFO - Processed 96300000 reads so far
2011-05-19 19:14:07,318 - INFO - Processed 96400000 reads so far
2011-05-19 19:14:16,932 - INFO - Processed 96500000 reads so far
2011-05-19 19:14:27,630 - INFO - Processed 96600000 reads so far
2011-05-19 19:14:37,694 - INFO - Processed 96700000 reads so far
2011-05-19 19:14:46,213 - INFO - Processed 96800000 reads so far
2011-05-19 19:14:46,600 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:102990590-123010590
2011-05-19 19:14:58,263 - INFO - Processed 96900000 reads so far
2011-05-19 19:15:08,882 - INFO - Processed 97000000 reads so far
2011-05-19 19:15:18,223 - INFO - Processed 97100000 reads so far
2011-05-19 19:15:27,242 - INFO - Processed 97200000 reads so far
2011-05-19 19:15:39,687 - INFO - Processed 97300000 reads so far
2011-05-19 19:15:51,185 - INFO - Processed 97400000 reads so far
2011-05-19 19:16:01,335 - INFO - Processed 97500000 reads so far
2011-05-19 19:16:12,353 - INFO - Processed 97600000 reads so far
2011-05-19 19:16:26,312 - INFO - Processed 97700000 reads so far
2011-05-19 19:16:41,113 - INFO - Processed 97800000 reads so far
2011-05-19 19:16:41,215 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:122990592-143010592
2011-05-19 19:16:54,324 - INFO - Processed 97900000 reads so far
2011-05-19 19:17:07,224 - INFO - Processed 98000000 reads so far
2011-05-19 19:17:18,531 - INFO - Processed 98100000 reads so far
2011-05-19 19:17:32,536 - INFO - Processed 98200000 reads so far
2011-05-19 19:17:44,095 - INFO - Processed 98300000 reads so far
2011-05-19 19:17:56,324 - INFO - Processed 98400000 reads so far
2011-05-19 19:18:08,060 - INFO - Processed 98500000 reads so far
2011-05-19 19:18:20,980 - INFO - Processed 98600000 reads so far
2011-05-19 19:18:34,674 - INFO - Processed 98700000 reads so far
2011-05-19 19:18:45,132 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5:142990602-163010602
2011-05-19 19:18:46,197 - INFO - Processed 98800000 reads so far
2011-05-19 19:18:57,748 - INFO - Processed 98900000 reads so far
2011-05-19 19:19:11,332 - INFO - Processed 99000000 reads so far
2011-05-19 19:19:22,767 - INFO - Processed 99100000 reads so far
2011-05-19 19:19:35,292 - INFO - Processed 99200000 reads so far
2011-05-19 19:19:44,291 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr5_random:0-20010033
2011-05-19 19:19:44,787 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:2989997-23009997
2011-05-19 19:19:49,209 - INFO - Processed 99300000 reads so far
2011-05-19 19:20:04,267 - INFO - Processed 99400000 reads so far
2011-05-19 19:20:15,810 - INFO - Processed 99500000 reads so far
2011-05-19 19:20:27,502 - INFO - Processed 99600000 reads so far
2011-05-19 19:20:38,932 - INFO - Processed 99700000 reads so far
2011-05-19 19:20:52,232 - INFO - Processed 99800000 reads so far
2011-05-19 19:21:03,543 - INFO - Processed 99900000 reads so far
2011-05-19 19:21:15,115 - INFO - Processed 100000000 reads so far
2011-05-19 19:21:27,191 - INFO - Processed 100100000 reads so far
2011-05-19 19:21:40,161 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:22990004-43010004
2011-05-19 19:21:40,558 - INFO - Processed 100200000 reads so far
2011-05-19 19:21:51,861 - INFO - Processed 100300000 reads so far
2011-05-19 19:22:02,516 - INFO - Processed 100400000 reads so far
2011-05-19 19:22:14,354 - INFO - Processed 100500000 reads so far
2011-05-19 19:22:23,051 - INFO - Processed 100600000 reads so far
2011-05-19 19:22:31,467 - INFO - Processed 100700000 reads so far
2011-05-19 19:22:43,105 - INFO - Processed 100800000 reads so far
2011-05-19 19:22:53,370 - INFO - Processed 100900000 reads so far
2011-05-19 19:23:05,348 - INFO - Processed 101000000 reads so far
2011-05-19 19:23:17,104 - INFO - Processed 101100000 reads so far
2011-05-19 19:23:27,510 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:42990062-63010062
2011-05-19 19:23:31,029 - INFO - Processed 101200000 reads so far
2011-05-19 19:23:41,821 - INFO - Processed 101300000 reads so far
2011-05-19 19:23:50,512 - INFO - Processed 101400000 reads so far
2011-05-19 19:24:00,304 - INFO - Processed 101500000 reads so far
2011-05-19 19:24:09,171 - INFO - Processed 101600000 reads so far
2011-05-19 19:24:19,488 - INFO - Processed 101700000 reads so far
2011-05-19 19:24:33,240 - INFO - Processed 101800000 reads so far
2011-05-19 19:24:45,445 - INFO - Processed 101900000 reads so far
2011-05-19 19:24:56,352 - INFO - Processed 102000000 reads so far
2011-05-19 19:25:07,786 - INFO - Processed 102100000 reads so far
2011-05-19 19:25:14,744 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:62990073-83010073
2011-05-19 19:25:20,006 - INFO - Processed 102200000 reads so far
2011-05-19 19:25:32,311 - INFO - Processed 102300000 reads so far
2011-05-19 19:25:47,350 - INFO - Processed 102400000 reads so far
2011-05-19 19:26:00,190 - INFO - Processed 102500000 reads so far
2011-05-19 19:26:13,622 - INFO - Processed 102600000 reads so far
2011-05-19 19:26:26,466 - INFO - Processed 102700000 reads so far
2011-05-19 19:26:38,005 - INFO - Processed 102800000 reads so far
2011-05-19 19:26:51,697 - INFO - Processed 102900000 reads so far
2011-05-19 19:27:02,658 - INFO - Processed 103000000 reads so far
2011-05-19 19:27:11,980 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:82990110-103010110
2011-05-19 19:27:13,738 - INFO - Processed 103100000 reads so far
2011-05-19 19:27:26,392 - INFO - Processed 103200000 reads so far
2011-05-19 19:27:39,421 - INFO - Processed 103300000 reads so far
2011-05-19 19:27:50,886 - INFO - Processed 103400000 reads so far
2011-05-19 19:28:06,557 - INFO - Processed 103500000 reads so far
2011-05-19 19:28:18,631 - INFO - Processed 103600000 reads so far
2011-05-19 19:28:32,024 - INFO - Processed 103700000 reads so far
2011-05-19 19:28:44,856 - INFO - Processed 103800000 reads so far
2011-05-19 19:28:56,091 - INFO - Processed 103900000 reads so far
2011-05-19 19:29:07,467 - INFO - Processed 104000000 reads so far
2011-05-19 19:29:19,776 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:102990117-123010117
2011-05-19 19:29:21,861 - INFO - Processed 104100000 reads so far
2011-05-19 19:29:31,559 - INFO - Processed 104200000 reads so far
2011-05-19 19:29:41,247 - INFO - Processed 104300000 reads so far
2011-05-19 19:29:52,017 - INFO - Processed 104400000 reads so far
2011-05-19 19:30:02,824 - INFO - Processed 104500000 reads so far
2011-05-19 19:30:12,390 - INFO - Processed 104600000 reads so far
2011-05-19 19:30:23,615 - INFO - Processed 104700000 reads so far
2011-05-19 19:30:33,910 - INFO - Processed 104800000 reads so far
2011-05-19 19:30:43,258 - INFO - Processed 104900000 reads so far
2011-05-19 19:30:52,027 - INFO - Processed 105000000 reads so far
2011-05-19 19:31:04,275 - INFO - Processed 105100000 reads so far
2011-05-19 19:31:14,544 - INFO - Processed 105200000 reads so far
2011-05-19 19:31:25,787 - INFO - Processed 105300000 reads so far
2011-05-19 19:31:40,075 - INFO - Processed 105400000 reads so far
2011-05-19 19:31:51,799 - INFO - Processed 105500000 reads so far
2011-05-19 19:32:07,558 - INFO - Processed 105600000 reads so far
2011-05-19 19:32:20,476 - INFO - Processed 105700000 reads so far
2011-05-19 19:32:33,823 - INFO - Processed 105800000 reads so far
2011-05-19 19:32:50,745 - INFO - Processed 105900000 reads so far
2011-05-19 19:32:56,142 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:122990186-143010186
2011-05-19 19:33:02,652 - INFO - Processed 106000000 reads so far
2011-05-19 19:33:13,295 - INFO - Processed 106100000 reads so far
2011-05-19 19:33:25,005 - INFO - Processed 106200000 reads so far
2011-05-19 19:33:35,222 - INFO - Processed 106300000 reads so far
2011-05-19 19:33:44,212 - INFO - Processed 106400000 reads so far
2011-05-19 19:33:55,502 - INFO - Processed 106500000 reads so far
2011-05-19 19:34:07,556 - INFO - Processed 106600000 reads so far
2011-05-19 19:34:19,683 - INFO - Processed 106700000 reads so far
2011-05-19 19:34:31,563 - INFO - Processed 106800000 reads so far
2011-05-19 19:34:40,337 - INFO - Processed 106900000 reads so far
2011-05-19 19:34:44,438 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr6:142990192-163010192
2011-05-19 19:34:50,577 - INFO - Processed 107000000 reads so far
2011-05-19 19:35:00,550 - INFO - Processed 107100000 reads so far
2011-05-19 19:35:09,291 - INFO - Processed 107200000 reads so far
2011-05-19 19:35:15,325 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:2990257-23010257
2011-05-19 19:35:18,371 - INFO - Processed 107300000 reads so far
2011-05-19 19:35:28,266 - INFO - Processed 107400000 reads so far
2011-05-19 19:35:38,040 - INFO - Processed 107500000 reads so far
2011-05-19 19:35:46,488 - INFO - Processed 107600000 reads so far
2011-05-19 19:35:55,276 - INFO - Processed 107700000 reads so far
2011-05-19 19:36:05,269 - INFO - Processed 107800000 reads so far
2011-05-19 19:36:17,247 - INFO - Processed 107900000 reads so far
2011-05-19 19:36:30,462 - INFO - Processed 108000000 reads so far
2011-05-19 19:36:41,415 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:22990347-43010347
2011-05-19 19:36:41,593 - INFO - Processed 108100000 reads so far
2011-05-19 19:36:53,173 - INFO - Processed 108200000 reads so far
2011-05-19 19:37:04,402 - INFO - Processed 108300000 reads so far
2011-05-19 19:37:17,426 - INFO - Processed 108400000 reads so far
2011-05-19 19:37:29,089 - INFO - Processed 108500000 reads so far
2011-05-19 19:37:40,653 - INFO - Processed 108600000 reads so far
2011-05-19 19:37:51,868 - INFO - Processed 108700000 reads so far
2011-05-19 19:38:04,055 - INFO - Processed 108800000 reads so far
2011-05-19 19:38:13,710 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:46352843-66372843
2011-05-19 19:38:17,076 - INFO - Processed 108900000 reads so far
2011-05-19 19:38:27,680 - INFO - Processed 109000000 reads so far
2011-05-19 19:38:40,327 - INFO - Processed 109100000 reads so far
2011-05-19 19:38:49,813 - INFO - Processed 109200000 reads so far
2011-05-19 19:38:58,262 - INFO - Processed 109300000 reads so far
2011-05-19 19:39:07,363 - INFO - Processed 109400000 reads so far
2011-05-19 19:39:15,993 - INFO - Processed 109500000 reads so far
2011-05-19 19:39:28,990 - INFO - Processed 109600000 reads so far
2011-05-19 19:39:39,172 - INFO - Processed 109700000 reads so far
2011-05-19 19:39:49,710 - INFO - Processed 109800000 reads so far
2011-05-19 19:39:50,903 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:66352915-86372915
2011-05-19 19:40:00,544 - INFO - Processed 109900000 reads so far
2011-05-19 19:40:39,777 - INFO - Processed 110000000 reads so far
2011-05-19 19:40:50,569 - INFO - Processed 110100000 reads so far
2011-05-19 19:41:01,198 - INFO - Processed 110200000 reads so far
2011-05-19 19:41:12,243 - INFO - Processed 110300000 reads so far
2011-05-19 19:41:23,001 - INFO - Processed 110400000 reads so far
2011-05-19 19:41:33,138 - INFO - Processed 110500000 reads so far
2011-05-19 19:41:46,493 - INFO - Processed 110600000 reads so far
2011-05-19 19:41:57,943 - INFO - Processed 110700000 reads so far
2011-05-19 19:42:11,361 - INFO - Processed 110800000 reads so far
2011-05-19 19:42:12,880 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:86352990-106372990
2011-05-19 19:42:25,161 - INFO - Processed 110900000 reads so far
2011-05-19 19:42:37,436 - INFO - Processed 111000000 reads so far
2011-05-19 19:42:51,213 - INFO - Processed 111100000 reads so far
2011-05-19 19:43:00,707 - INFO - Processed 111200000 reads so far
2011-05-19 19:43:11,448 - INFO - Processed 111300000 reads so far
2011-05-19 19:43:22,491 - INFO - Processed 111400000 reads so far
2011-05-19 19:43:32,658 - INFO - Processed 111500000 reads so far
2011-05-19 19:43:40,498 - INFO - Processed 111600000 reads so far
2011-05-19 19:43:50,166 - INFO - Processed 111700000 reads so far
2011-05-19 19:44:01,626 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:106353009-126373009
2011-05-19 19:44:05,269 - INFO - Processed 111800000 reads so far
2011-05-19 19:44:16,063 - INFO - Processed 111900000 reads so far
2011-05-19 19:44:26,441 - INFO - Processed 112000000 reads so far
2011-05-19 19:44:40,440 - INFO - Processed 112100000 reads so far
2011-05-19 19:44:50,734 - INFO - Processed 112200000 reads so far
2011-05-19 19:45:01,632 - INFO - Processed 112300000 reads so far
2011-05-19 19:45:16,680 - INFO - Processed 112400000 reads so far
2011-05-19 19:45:27,492 - INFO - Processed 112500000 reads so far
2011-05-19 19:45:39,801 - INFO - Processed 112600000 reads so far
2011-05-19 19:45:51,900 - INFO - Processed 112700000 reads so far
2011-05-19 19:45:57,883 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:126353069-146373069
2011-05-19 19:46:04,308 - INFO - Processed 112800000 reads so far
2011-05-19 19:46:19,397 - INFO - Processed 112900000 reads so far
2011-05-19 19:46:34,644 - INFO - Processed 113000000 reads so far
2011-05-19 19:46:47,127 - INFO - Processed 113100000 reads so far
2011-05-19 19:46:58,301 - INFO - Processed 113200000 reads so far
2011-05-19 19:47:09,029 - INFO - Processed 113300000 reads so far
2011-05-19 19:47:19,437 - INFO - Processed 113400000 reads so far
2011-05-19 19:47:31,538 - INFO - Processed 113500000 reads so far
2011-05-19 19:47:41,163 - INFO - Processed 113600000 reads so far
2011-05-19 19:47:50,723 - INFO - Processed 113700000 reads so far
2011-05-19 19:47:58,027 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7:146353074-166373074
2011-05-19 19:48:02,273 - INFO - Processed 113800000 reads so far
2011-05-19 19:48:13,737 - INFO - Processed 113900000 reads so far
2011-05-19 19:48:22,480 - INFO - Processed 114000000 reads so far
2011-05-19 19:48:32,775 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr7_random:0-20010136
2011-05-19 19:48:33,756 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:2990001-23010001
2011-05-19 19:48:34,279 - INFO - Processed 114100000 reads so far
2011-05-19 19:48:43,681 - INFO - Processed 114200000 reads so far
2011-05-19 19:48:52,294 - INFO - Processed 114300000 reads so far
2011-05-19 19:49:02,814 - INFO - Processed 114400000 reads so far
2011-05-19 19:49:12,928 - INFO - Processed 114500000 reads so far
2011-05-19 19:49:24,010 - INFO - Processed 114600000 reads so far
2011-05-19 19:49:34,907 - INFO - Processed 114700000 reads so far
2011-05-19 19:49:49,248 - INFO - Processed 114800000 reads so far
2011-05-19 19:49:59,116 - INFO - Processed 114900000 reads so far
2011-05-19 19:50:07,225 - INFO - Processed 115000000 reads so far
2011-05-19 19:50:15,359 - INFO - Processed 115100000 reads so far
2011-05-19 19:50:23,628 - INFO - Processed 115200000 reads so far
2011-05-19 19:50:31,560 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:22990057-43010057
2011-05-19 19:50:33,484 - INFO - Processed 115300000 reads so far
2011-05-19 19:50:45,132 - INFO - Processed 115400000 reads so far
2011-05-19 19:50:56,919 - INFO - Processed 115500000 reads so far
2011-05-19 19:51:11,349 - INFO - Processed 115600000 reads so far
2011-05-19 19:51:22,695 - INFO - Processed 115700000 reads so far
2011-05-19 19:51:34,960 - INFO - Processed 115800000 reads so far
2011-05-19 19:51:47,358 - INFO - Processed 115900000 reads so far
2011-05-19 19:52:02,241 - INFO - Processed 116000000 reads so far
2011-05-19 19:52:13,375 - INFO - Processed 116100000 reads so far
2011-05-19 19:52:26,699 - INFO - Processed 116200000 reads so far
2011-05-19 19:52:29,849 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:42990061-63010061
2011-05-19 19:52:39,068 - INFO - Processed 116300000 reads so far
2011-05-19 19:52:50,388 - INFO - Processed 116400000 reads so far
2011-05-19 19:53:02,489 - INFO - Processed 116500000 reads so far
2011-05-19 19:53:17,434 - INFO - Processed 116600000 reads so far
2011-05-19 19:53:29,364 - INFO - Processed 116700000 reads so far
2011-05-19 19:53:40,548 - INFO - Processed 116800000 reads so far
2011-05-19 19:53:53,816 - INFO - Processed 116900000 reads so far
2011-05-19 19:54:05,331 - INFO - Processed 117000000 reads so far
2011-05-19 19:54:14,278 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:62990075-83010075
2011-05-19 19:54:17,017 - INFO - Processed 117100000 reads so far
2011-05-19 19:54:28,537 - INFO - Processed 117200000 reads so far
2011-05-19 19:54:40,509 - INFO - Processed 117300000 reads so far
2011-05-19 19:54:52,176 - INFO - Processed 117400000 reads so far
2011-05-19 19:55:05,105 - INFO - Processed 117500000 reads so far
2011-05-19 19:55:16,565 - INFO - Processed 117600000 reads so far
2011-05-19 19:55:27,727 - INFO - Processed 117700000 reads so far
2011-05-19 19:55:40,298 - INFO - Processed 117800000 reads so far
2011-05-19 19:55:51,732 - INFO - Processed 117900000 reads so far
2011-05-19 19:56:06,350 - INFO - Processed 118000000 reads so far
2011-05-19 19:56:12,979 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:82990093-103010093
2011-05-19 19:56:18,358 - INFO - Processed 118100000 reads so far
2011-05-19 19:56:29,848 - INFO - Processed 118200000 reads so far
2011-05-19 19:56:41,131 - INFO - Processed 118300000 reads so far
2011-05-19 19:56:51,836 - INFO - Processed 118400000 reads so far
2011-05-19 19:57:01,376 - INFO - Processed 118500000 reads so far
2011-05-19 19:57:13,239 - INFO - Processed 118600000 reads so far
2011-05-19 19:57:22,420 - INFO - Processed 118700000 reads so far
2011-05-19 19:57:33,660 - INFO - Processed 118800000 reads so far
2011-05-19 19:57:43,982 - INFO - Processed 118900000 reads so far
2011-05-19 19:57:56,231 - INFO - Processed 119000000 reads so far
2011-05-19 19:57:58,269 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:102990101-123010101
2011-05-19 19:58:05,496 - INFO - Processed 119100000 reads so far
2011-05-19 19:58:15,047 - INFO - Processed 119200000 reads so far
2011-05-19 19:58:25,815 - INFO - Processed 119300000 reads so far
2011-05-19 19:58:38,585 - INFO - Processed 119400000 reads so far
2011-05-19 19:58:54,243 - INFO - Processed 119500000 reads so far
2011-05-19 19:59:07,048 - INFO - Processed 119600000 reads so far
2011-05-19 19:59:18,599 - INFO - Processed 119700000 reads so far
2011-05-19 19:59:29,140 - INFO - Processed 119800000 reads so far
2011-05-19 19:59:44,650 - INFO - Processed 119900000 reads so far
2011-05-19 19:59:54,518 - INFO - Processed 120000000 reads so far
2011-05-19 19:59:54,841 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8:122990118-143010118
2011-05-19 20:00:04,826 - INFO - Processed 120100000 reads so far
2011-05-19 20:00:14,244 - INFO - Processed 120200000 reads so far
2011-05-19 20:00:25,988 - INFO - Processed 120300000 reads so far
2011-05-19 20:00:39,278 - INFO - Processed 120400000 reads so far
2011-05-19 20:00:43,778 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr8_random:0-20010064
2011-05-19 20:00:48,565 - INFO - Processed 120500000 reads so far
2011-05-19 20:00:56,154 - INFO - Processed 120600000 reads so far
2011-05-19 20:00:57,638 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:2989962-23009962
2011-05-19 20:01:04,493 - INFO - Processed 120700000 reads so far
2011-05-19 20:01:13,398 - INFO - Processed 120800000 reads so far
2011-05-19 20:01:24,041 - INFO - Processed 120900000 reads so far
2011-05-19 20:01:36,629 - INFO - Processed 121000000 reads so far
2011-05-19 20:01:48,095 - INFO - Processed 121100000 reads so far
2011-05-19 20:01:56,905 - INFO - Processed 121200000 reads so far
2011-05-19 20:02:06,174 - INFO - Processed 121300000 reads so far
2011-05-19 20:02:13,510 - INFO - Processed 121400000 reads so far
2011-05-19 20:02:20,703 - INFO - Processed 121500000 reads so far
2011-05-19 20:02:29,310 - INFO - Processed 121600000 reads so far
2011-05-19 20:02:40,747 - INFO - Processed 121700000 reads so far
2011-05-19 20:02:46,779 - INFO - Processed 121800000 reads so far
2011-05-19 20:02:55,969 - INFO - Processed 121900000 reads so far
2011-05-19 20:03:01,646 - INFO - Processed 122000000 reads so far
2011-05-19 20:03:08,955 - INFO - Processed 122100000 reads so far
2011-05-19 20:03:19,405 - INFO - Processed 122200000 reads so far
2011-05-19 20:03:33,371 - INFO - Processed 122300000 reads so far
2011-05-19 20:03:44,359 - INFO - Processed 122400000 reads so far
2011-05-19 20:03:53,764 - INFO - Processed 122500000 reads so far
2011-05-19 20:04:02,553 - INFO - Processed 122600000 reads so far
2011-05-19 20:04:10,153 - INFO - Processed 122700000 reads so far
2011-05-19 20:04:17,360 - INFO - Processed 122800000 reads so far
2011-05-19 20:04:26,892 - INFO - Processed 122900000 reads so far
2011-05-19 20:04:33,295 - INFO - Processed 123000000 reads so far
2011-05-19 20:04:40,757 - INFO - Processed 123100000 reads so far
2011-05-19 20:04:48,274 - INFO - Processed 123200000 reads so far
2011-05-19 20:04:56,323 - INFO - Processed 123300000 reads so far
2011-05-19 20:05:02,492 - INFO - Processed 123400000 reads so far
2011-05-19 20:05:10,680 - INFO - Processed 123500000 reads so far
2011-05-19 20:05:17,132 - INFO - Processed 123600000 reads so far
2011-05-19 20:05:24,746 - INFO - Processed 123700000 reads so far
2011-05-19 20:05:33,271 - INFO - Processed 123800000 reads so far
2011-05-19 20:05:40,737 - INFO - Processed 123900000 reads so far
2011-05-19 20:05:49,309 - INFO - Processed 124000000 reads so far
2011-05-19 20:05:59,863 - INFO - Processed 124100000 reads so far
2011-05-19 20:06:08,115 - INFO - Processed 124200000 reads so far
2011-05-19 20:06:17,003 - INFO - Processed 124300000 reads so far
2011-05-19 20:06:26,694 - INFO - Processed 124400000 reads so far
2011-05-19 20:06:37,194 - INFO - Processed 124500000 reads so far
2011-05-19 20:06:45,247 - INFO - Processed 124600000 reads so far
2011-05-19 20:06:53,617 - INFO - Processed 124700000 reads so far
2011-05-19 20:07:01,026 - INFO - Processed 124800000 reads so far
2011-05-19 20:07:07,538 - INFO - Processed 124900000 reads so far
2011-05-19 20:07:15,086 - INFO - Processed 125000000 reads so far
2011-05-19 20:07:24,512 - INFO - Processed 125100000 reads so far
2011-05-19 20:07:34,257 - INFO - Processed 125200000 reads so far
2011-05-19 20:07:42,203 - INFO - Processed 125300000 reads so far
2011-05-19 20:07:49,324 - INFO - Processed 125400000 reads so far
2011-05-19 20:07:56,626 - INFO - Processed 125500000 reads so far
2011-05-19 20:08:04,520 - INFO - Processed 125600000 reads so far
2011-05-19 20:08:11,838 - INFO - Processed 125700000 reads so far
2011-05-19 20:08:20,296 - INFO - Processed 125800000 reads so far
2011-05-19 20:08:27,171 - INFO - Processed 125900000 reads so far
2011-05-19 20:08:33,824 - INFO - Processed 126000000 reads so far
2011-05-19 20:08:41,385 - INFO - Processed 126100000 reads so far
2011-05-19 20:08:51,309 - INFO - Processed 126200000 reads so far
2011-05-19 20:09:00,140 - INFO - Processed 126300000 reads so far
2011-05-19 20:09:07,275 - INFO - Processed 126400000 reads so far
2011-05-19 20:09:15,942 - INFO - Processed 126500000 reads so far
2011-05-19 20:09:25,365 - INFO - Processed 126600000 reads so far
2011-05-19 20:09:34,985 - INFO - Processed 126700000 reads so far
2011-05-19 20:09:43,221 - INFO - Processed 126800000 reads so far
2011-05-19 20:09:53,528 - INFO - Processed 126900000 reads so far
2011-05-19 20:10:03,635 - INFO - Processed 127000000 reads so far
2011-05-19 20:10:15,726 - INFO - Processed 127100000 reads so far
2011-05-19 20:10:26,865 - INFO - Processed 127200000 reads so far
2011-05-19 20:10:39,237 - INFO - Processed 127300000 reads so far
2011-05-19 20:10:51,442 - INFO - Processed 127400000 reads so far
2011-05-19 20:11:03,014 - INFO - Processed 127500000 reads so far
2011-05-19 20:11:14,093 - INFO - Processed 127600000 reads so far
2011-05-19 20:11:23,236 - INFO - Processed 127700000 reads so far
2011-05-19 20:11:33,122 - INFO - Processed 127800000 reads so far
2011-05-19 20:11:35,171 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:22989972-43009972
2011-05-19 20:11:45,468 - INFO - Processed 127900000 reads so far
2011-05-19 20:11:59,342 - INFO - Processed 128000000 reads so far
2011-05-19 20:12:11,784 - INFO - Processed 128100000 reads so far
2011-05-19 20:12:22,576 - INFO - Processed 128200000 reads so far
2011-05-19 20:12:34,086 - INFO - Processed 128300000 reads so far
2011-05-19 20:12:45,649 - INFO - Processed 128400000 reads so far
2011-05-19 20:12:53,642 - INFO - Processed 128500000 reads so far
2011-05-19 20:13:04,367 - INFO - Processed 128600000 reads so far
2011-05-19 20:13:15,513 - INFO - Processed 128700000 reads so far
2011-05-19 20:13:26,669 - INFO - Processed 128800000 reads so far
2011-05-19 20:13:38,924 - INFO - Processed 128900000 reads so far
2011-05-19 20:13:40,930 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:42989974-63009974
2011-05-19 20:13:52,009 - INFO - Processed 129000000 reads so far
2011-05-19 20:14:02,770 - INFO - Processed 129100000 reads so far
2011-05-19 20:14:14,704 - INFO - Processed 129200000 reads so far
2011-05-19 20:14:25,547 - INFO - Processed 129300000 reads so far
2011-05-19 20:14:38,201 - INFO - Processed 129400000 reads so far
2011-05-19 20:14:49,978 - INFO - Processed 129500000 reads so far
2011-05-19 20:15:01,614 - INFO - Processed 129600000 reads so far
2011-05-19 20:15:13,842 - INFO - Processed 129700000 reads so far
2011-05-19 20:15:26,051 - INFO - Processed 129800000 reads so far
2011-05-19 20:15:37,400 - INFO - Processed 129900000 reads so far
2011-05-19 20:15:39,000 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:62989983-83009983
2011-05-19 20:15:55,999 - INFO - Processed 130000000 reads so far
2011-05-19 20:16:07,766 - INFO - Processed 130100000 reads so far
2011-05-19 20:16:19,561 - INFO - Processed 130200000 reads so far
2011-05-19 20:16:35,835 - INFO - Processed 130300000 reads so far
2011-05-19 20:16:48,283 - INFO - Processed 130400000 reads so far
2011-05-19 20:16:59,640 - INFO - Processed 130500000 reads so far
2011-05-19 20:17:12,747 - INFO - Processed 130600000 reads so far
2011-05-19 20:17:22,624 - INFO - Processed 130700000 reads so far
2011-05-19 20:17:33,220 - INFO - Processed 130800000 reads so far
2011-05-19 20:17:40,718 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:82989995-103009995
2011-05-19 20:17:43,352 - INFO - Processed 130900000 reads so far
2011-05-19 20:17:56,520 - INFO - Processed 131000000 reads so far
2011-05-19 20:18:09,731 - INFO - Processed 131100000 reads so far
2011-05-19 20:18:22,572 - INFO - Processed 131200000 reads so far
2011-05-19 20:18:34,911 - INFO - Processed 131300000 reads so far
2011-05-19 20:18:44,527 - INFO - Processed 131400000 reads so far
2011-05-19 20:18:54,441 - INFO - Processed 131500000 reads so far
2011-05-19 20:19:05,090 - INFO - Processed 131600000 reads so far
2011-05-19 20:19:15,754 - INFO - Processed 131700000 reads so far
2011-05-19 20:19:28,153 - INFO - Processed 131800000 reads so far
2011-05-19 20:19:35,404 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:102990001-123010001
2011-05-19 20:19:41,170 - INFO - Processed 131900000 reads so far
2011-05-19 20:19:52,691 - INFO - Processed 132000000 reads so far
2011-05-19 20:20:05,608 - INFO - Processed 132100000 reads so far
2011-05-19 20:20:15,286 - INFO - Processed 132200000 reads so far
2011-05-19 20:20:26,858 - INFO - Processed 132300000 reads so far
2011-05-19 20:20:39,751 - INFO - Processed 132400000 reads so far
2011-05-19 20:20:50,441 - INFO - Processed 132500000 reads so far
2011-05-19 20:21:00,683 - INFO - Processed 132600000 reads so far
2011-05-19 20:21:19,585 - INFO - Processed 132700000 reads so far
2011-05-19 20:21:29,149 - INFO - Processed 132800000 reads so far
2011-05-19 20:21:34,295 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9:122990006-143010006
2011-05-19 20:21:38,320 - INFO - Processed 132900000 reads so far
2011-05-19 20:21:39,526 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chr9_random:0-20010005
2011-05-19 20:21:46,070 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrM:0-20010000
2011-05-19 20:21:51,419 - INFO - Processed 133000000 reads so far
2011-05-19 20:21:51,822 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrUn_random:0-20010001
2011-05-19 20:22:03,918 - INFO - Processed 133100000 reads so far
2011-05-19 20:22:13,605 - INFO - Processed 133200000 reads so far
2011-05-19 20:22:23,772 - INFO - Processed 133300000 reads so far
2011-05-19 20:22:33,186 - INFO - Processed 133400000 reads so far
2011-05-19 20:22:33,639 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:2989999-23009999
2011-05-19 20:22:43,677 - INFO - Processed 133500000 reads so far
2011-05-19 20:22:58,084 - INFO - Processed 133600000 reads so far
2011-05-19 20:23:08,041 - INFO - Processed 133700000 reads so far
2011-05-19 20:23:15,868 - INFO - Processed 133800000 reads so far
2011-05-19 20:23:25,100 - INFO - Processed 133900000 reads so far
2011-05-19 20:23:33,734 - INFO - Processed 134000000 reads so far
2011-05-19 20:23:41,235 - INFO - Processed 134100000 reads so far
2011-05-19 20:23:49,690 - INFO - Processed 134200000 reads so far
2011-05-19 20:23:57,090 - INFO - Processed 134300000 reads so far
2011-05-19 20:24:11,327 - INFO - Processed 134400000 reads so far
2011-05-19 20:24:22,167 - INFO - Processed 134500000 reads so far
2011-05-19 20:24:28,374 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:22990000-43010000
2011-05-19 20:24:34,079 - INFO - Processed 134600000 reads so far
2011-05-19 20:24:47,199 - INFO - Processed 134700000 reads so far
2011-05-19 20:24:58,432 - INFO - Processed 134800000 reads so far
2011-05-19 20:25:06,017 - INFO - Processed 134900000 reads so far
2011-05-19 20:25:14,672 - INFO - Processed 135000000 reads so far
2011-05-19 20:25:24,473 - INFO - Processed 135100000 reads so far
2011-05-19 20:25:32,110 - INFO - Processed 135200000 reads so far
2011-05-19 20:25:41,005 - INFO - Processed 135300000 reads so far
2011-05-19 20:25:50,603 - INFO - Processed 135400000 reads so far
2011-05-19 20:26:00,250 - INFO - Processed 135500000 reads so far
2011-05-19 20:26:07,947 - INFO - Processed 135600000 reads so far
2011-05-19 20:26:17,392 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:42990002-63010002
2011-05-19 20:26:20,426 - INFO - Processed 135700000 reads so far
2011-05-19 20:26:33,719 - INFO - Processed 135800000 reads so far
2011-05-19 20:26:47,025 - INFO - Processed 135900000 reads so far
2011-05-19 20:26:59,747 - INFO - Processed 136000000 reads so far
2011-05-19 20:27:11,837 - INFO - Processed 136100000 reads so far
2011-05-19 20:27:25,772 - INFO - Processed 136200000 reads so far
2011-05-19 20:27:38,353 - INFO - Processed 136300000 reads so far
2011-05-19 20:27:49,662 - INFO - Processed 136400000 reads so far
2011-05-19 20:28:09,806 - INFO - Processed 136500000 reads so far
2011-05-19 20:28:21,353 - INFO - Processed 136600000 reads so far
2011-05-19 20:28:24,741 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:62990025-83010025
2011-05-19 20:28:36,665 - INFO - Processed 136700000 reads so far
2011-05-19 20:28:50,016 - INFO - Processed 136800000 reads so far
2011-05-19 20:29:01,400 - INFO - Processed 136900000 reads so far
2011-05-19 20:29:13,276 - INFO - Processed 137000000 reads so far
2011-05-19 20:29:24,603 - INFO - Processed 137100000 reads so far
2011-05-19 20:29:35,845 - INFO - Processed 137200000 reads so far
2011-05-19 20:29:45,594 - INFO - Processed 137300000 reads so far
2011-05-19 20:29:54,072 - INFO - Processed 137400000 reads so far
2011-05-19 20:30:05,505 - INFO - Processed 137500000 reads so far
2011-05-19 20:30:12,843 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:82990028-103010028
2011-05-19 20:30:16,626 - INFO - Processed 137600000 reads so far
2011-05-19 20:30:27,408 - INFO - Processed 137700000 reads so far
2011-05-19 20:30:38,644 - INFO - Processed 137800000 reads so far
2011-05-19 20:30:49,560 - INFO - Processed 137900000 reads so far
2011-05-19 20:31:00,505 - INFO - Processed 138000000 reads so far
2011-05-19 20:31:09,202 - INFO - Processed 138100000 reads so far
2011-05-19 20:31:19,106 - INFO - Processed 138200000 reads so far
2011-05-19 20:31:28,503 - INFO - Processed 138300000 reads so far
2011-05-19 20:31:38,867 - INFO - Processed 138400000 reads so far
2011-05-19 20:31:49,058 - INFO - Processed 138500000 reads so far
2011-05-19 20:31:49,621 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:102990056-123010056
2011-05-19 20:32:00,776 - INFO - Processed 138600000 reads so far
2011-05-19 20:32:08,873 - INFO - Processed 138700000 reads so far
2011-05-19 20:32:18,012 - INFO - Processed 138800000 reads so far
2011-05-19 20:32:28,600 - INFO - Processed 138900000 reads so far
2011-05-19 20:32:38,429 - INFO - Processed 139000000 reads so far
2011-05-19 20:32:46,462 - INFO - Processed 139100000 reads so far
2011-05-19 20:32:56,481 - INFO - Processed 139200000 reads so far
2011-05-19 20:33:05,737 - INFO - Processed 139300000 reads so far
2011-05-19 20:33:15,841 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:122990098-143010098
2011-05-19 20:33:17,484 - INFO - Processed 139400000 reads so far
2011-05-19 20:33:29,087 - INFO - Processed 139500000 reads so far
2011-05-19 20:33:37,161 - INFO - Processed 139600000 reads so far
2011-05-19 20:33:48,536 - INFO - Processed 139700000 reads so far
2011-05-19 20:33:59,901 - INFO - Processed 139800000 reads so far
2011-05-19 20:34:10,965 - INFO - Processed 139900000 reads so far
2011-05-19 20:34:21,281 - INFO - Processed 140000000 reads so far
2011-05-19 20:34:31,974 - INFO - Processed 140100000 reads so far
2011-05-19 20:34:40,170 - INFO - Processed 140200000 reads so far
2011-05-19 20:34:49,822 - INFO - Processed 140300000 reads so far
2011-05-19 20:35:00,582 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:142990106-163010106
2011-05-19 20:35:03,076 - INFO - Processed 140400000 reads so far
2011-05-19 20:35:12,525 - INFO - Processed 140500000 reads so far
2011-05-19 20:35:22,319 - INFO - Processed 140600000 reads so far
2011-05-19 20:35:34,435 - INFO - Processed 140700000 reads so far
2011-05-19 20:35:45,291 - INFO - Processed 140800000 reads so far
2011-05-19 20:35:55,896 - INFO - Processed 140900000 reads so far
2011-05-19 20:36:07,436 - INFO - Processed 141000000 reads so far
2011-05-19 20:36:17,621 - INFO - Processed 141100000 reads so far
2011-05-19 20:36:27,858 - INFO - Processed 141200000 reads so far
2011-05-19 20:36:36,840 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX:162990142-183010142
2011-05-19 20:36:37,230 - INFO - Processed 141300000 reads so far
2011-05-19 20:36:47,971 - INFO - Processed 141400000 reads so far
2011-05-19 20:36:57,933 - INFO - Processed 141500000 reads so far
2011-05-19 20:37:02,682 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrX_random:0-20010000
2011-05-19 20:37:06,705 - INFO - Processed 141600000 reads so far
2011-05-19 20:37:09,556 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY:921-20020921
2011-05-19 20:37:10,971 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:51947-20071947
2011-05-19 20:37:13,569 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:20124991-40144991
2011-05-19 20:37:15,436 - INFO - Constructing variant generator with minMapQ=0, minFlank=0, minBaseQual=5. Region = chrY_random:40171121-60191121
2011-05-19 20:37:18,040 - INFO - Processed 141700000 reads so far
2011-05-19 20:37:22,443 - INFO - Processed 141800000 reads so far
2011-05-19 20:37:27,178 - INFO - Processed 141900000 reads so far
2011-05-19 20:37:32,390 - INFO - Processed 142000000 reads so far
2011-05-19 20:37:36,731 - INFO - Processed 142100000 reads so far
2011-05-19 20:37:40,967 - INFO - Processed 142200000 reads so far
2011-05-19 20:37:45,518 - INFO - Processed 142300000 reads so far
2011-05-19 20:37:49,749 - INFO - Processed 142400000 reads so far
2011-05-19 20:37:53,409 - INFO - Processed 142500000 reads so far
2011-05-19 20:37:56,109 - INFO - Processed 142600000 reads so far
2011-05-19 20:38:00,699 - INFO - Processed 142700000 reads so far
2011-05-19 20:38:05,147 - INFO - Processed 142800000 reads so far
2011-05-19 20:38:09,170 - INFO - Processed 142900000 reads so far
2011-05-19 20:38:13,705 - INFO - Processed 143000000 reads so far
2011-05-19 20:38:18,924 - INFO - Processed 143100000 reads so far
2011-05-19 20:38:23,276 - INFO - Processed 143200000 reads so far
2011-05-19 20:38:27,561 - INFO - Processed 143300000 reads so far
2011-05-19 20:38:33,763 - INFO - Processed 143400000 reads so far
2011-05-19 20:38:38,216 - INFO - Processed 143500000 reads so far
2011-05-19 20:38:42,608 - INFO - Processed 143600000 reads so far
2011-05-19 20:38:44,995 - INFO - Finished loading data. Outputting QC metrics
2011-05-19 20:39:07,665 - INFO - Finished outputting QC metrics
2011-05-19 20:39:07,781 - INFO - Finished generating QC metrics